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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Morozov D., Mironov V., Moryachkov R. V., Shchugoreva I. A., Artyushenko P. V., Zamay G. S., Kolovskaya O. S., Zamay T. N., Krat A. V., Molodenskiy D. S., Zabluda V. N., Veprintsev D. V., Sokolov A. Е., Zukov R. A., Berezovski M. V., Tomilin F. N., Fedorov D. G., Alexeev Y., Kichkailo A. S.
Заглавие : The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer
Место публикации : Mol. Ther. Nucl. Acids. - 2021. - Vol. 25. - P.316-327. - ISSN 21622531 (ISSN), DOI 10.1016/j.omtn.2021.07.015
Примечания : Cited References: 84. - The research was performed using equipment of the Shared Core Facilities of Molecular and Cell Technologies at Krasnoyarsk State Medical University. The synchrotron SAXS data were collected at beamline P12 operated by EMBL Hamburg at the PETRA III storage ring (DESY, Hamburg, Germany). A.S.K. is grateful to Aptamerlab LLC for the assistance in aptamer design and 3D structure analyses. We thank Ivan Lapin for his help with microscopic analyses. Microscopic analyses using Carl Zeiss LSM 800 were carried out at the Center for Bioassay, Nanotechnology and Nanomaterials Safety (“Biotest-Nano”) (Multiple-Access Center, Tomsk State University, Tomsk, Russia). D.M. also thanks the CSC-IT Center in Espoo, Finland, for providing computational resources. The study was supported by a grant from the Russian Science Foundation (project number 21-73-20240) for A.S.K. R.V.M aknowledges Russian Foundation for Basic Research (project number 19-32-90266) for funding. D.G.F. acknowledges financial support by JSPS KAKENHI, grant number 19H02682. D.S.M. acknowledges financial support by BMBF grant number 16QK10A (SAS-BSOFT). Y.A.’s work at Argonne National Laboratory was supported by the US Department of Energy, Office of Science, under contract DE-AC02-06CH11357. D.M. received funding as a part of BioExcel CoE (https://bioexcel.eu/), a project funded by the European Union contracts H2020-INFRAEDI-02-2018-823830 and H2020-EINFRA-2015-1-675728. V.M. thanks Russian Foundation for Basic Research (project number 19-03-00043) for funding
Аннотация: Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Shchugoreva I. A., Artyushenko P. V., Tomilin F. N., Morozov D. I., Mironov V. A., Moryachkov R. V., Kichkailo A. S.
Заглавие : Applying joint theoretical experimental research to aptamer modeling
Место публикации : Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P.105-106. - ISSN 18199496 (ISSN), DOI 10.20333/2500136-2021-2-105-106; Сиб. мед. обозрение
Примечания : Cited References: 4
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. Obtain-ing 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.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Ozerskaya A. V., Zamay T. N., Kolovskaya O. S., Tokarev N. A., Belugin K. V., Chanchikova N. G., Badmaev O. N., Zamay G. S., Shchugoreva I. A., Moryachkov R. V., Zabluda V. N., Khorzhevskii V. A., Shepelevich N., Gappoev S. V., Karlova E. A., Saveleva A. S., Volzhentsev A. A., Blagodatova A. N., Lukyanenko K. A., Veprintsev D. V., Smolyarova T. E., Tomilin F. N., Zamay S. S., Silnikov V. N., Berezovski M. V., Kichkailo A. S.
Заглавие : 11C-radiolabeled aptamer for imaging of tumors and metastases using positron emission tomography-computed tomography
Место публикации : Mol. Ther. Nucl. Acids. - 2021. - Vol. 26. - P.1159-1172. - ISSN 21622531 (ISSN), DOI 10.1016/j.omtn.2021.10.020
Примечания : Cited References: 44
Аннотация: Identification of primary tumors and metastasis sites is an essential step in cancer diagnostics and the following treatment. Positron emission tomography-computed tomography (PET/CT) is one of the most reliable methods for scanning the whole organism for malignancies. In this work, we synthesized an 11C-labeled oligonucleotide primer and hybridized it to an anti-cancer DNA aptamer. The 11C-aptamer was applied for in vivo imaging of Ehrlich ascites carcinoma and its metastases in mice using PET/CT. The imaging experiments with the 11C-aptamer determined very small primary and secondary tumors of 3 mm2 and less. We also compared 11C imaging with the standard radiotracer, 2-deoxy-2-[fluorine-18]fluoro-D-glucose (18F-FDG), and found better selectivity of the 11C-aptamer to metastatic lesions in the metabolically active organs than 18F-FDG. 11C radionuclide with an ultra-short (20.38 min) half-life is considered safest for PET/CT imaging and does not cause false-positive results in heart imaging. Its combination with aptamers gives us high-specificity and high-contrast imaging of cancer cells and can be applied for PET/CT-guided drug delivery in cancer therapies.
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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Moryachkov R. V., Morozov D., Mironov V., Shchugoreva I., Artyushenko P. V., Zamay G. S., Molodenskiy D. S., Zabluda V. N., Kichkailo A.S., Sokolov A. Е.
Заглавие : The role of small-angle X-ray scattering and molecular simulations in 3D structure elucidation of a DNA aptamer-cancer cells magnetic separation agent
Коллективы : International Baltic Conference on Magnetism: focus on nanobiomedicine and smart materials, Балтийский федеральный университет им. И. Канта
Место публикации : 4th International Baltic Conference on Magnetism (IBCM 2021): Book of abstracts. - 2021. - P.168
Примечания : Cited References: 2. - The reported study was funded by RFBR, project number 19-32-90266
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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Moryachkov R. V., Zabluda V. N., Sokolov A. Е., Shchugoreva I. A., Tomilin F. N., Peters G., Spiridonova V. A.
Заглавие : Small-Angle scattering applications to the analysis of aptamer structure and conformational changes
Коллективы : Aptamers in Russia, international conference
Место публикации : Aptamers in Russia, international conference (1 ; 2019 ; Aug. 27-30 ; Krasnoyarsk). Molecular Therapy - Nucleic Acids: book of abstracts of the 1st Int. conf. "Aptamers in Russia 2019". - 2019. - Vol. 17, Suppl. 1. - P.4
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Вид документа : Статья из сборника (выпуск продолж. издания)
Шифр издания :
Автор(ы) : Moryachkov R. V., Zabluda V. N., Berlina A. N., Peters G. S., Kichkailo A. S., Sokolov A. Е.
Заглавие : Small-angle scattering applications to the analysis of aptamer structure and conformational changes
Коллективы : Internetional Conference on Synchrotron and Free Electron Laser Radiation: Generation and Application
Место публикации : Internetional Conference on Synchrotron and Free Electron Laser Radiation: Generation and Application (2020 ; 13-16 July ; Novosibirsk). AIP Conference Proceedings: book of abstracts. - 2020. - Vol. 2299. - Ст.040002. - , DOI 10.1063/5.0030394; \b Synchrotron and free electron laser radiation: generation and application (SFR-2020). - Novosibirsk. - P.45-46
Примечания : Cited References: 40. - The reported study was funded by RFBR, project number 19-32-90266 (investigation of the structure changes). This work was financially supported by Russian Science Foundation (project # 19-44-02020, obtaining of the complexes of aptamer and lead ions). We acknowledge the European Synchrotron Radiation Facility for provision of synchrotron radiation facilities (experiment #MX-2039) and we would like to thank Bart Van Laer for assistance in using beamline BM29
Аннотация: Aptamers, structured single-chain oligonucleotides, are promising tools for detection of a wide variety of compounds, from high to low molecular weight, and affecting on them. The aptamers that are most affine for a detectable compound are selected from the libraries of random sequences by the SELEX method (Systematic evolution of ligands by exponential enrichment). The reason why aptamers deserve a special consideration lies in the specific features of their structure and the mechanism of binding to their target. Aptamers can be exploited for metal-ion sensing, biosensing, drug delivery and other functions. To apply the oligonucleotides in the medicine, ecology, food production, agriculture, etc., we need to know how the aptamers bind to their targets, how they change their conformation upon specific binding and how the environment influences on the affinity of aptamers. Small-Angle X-ray scattering showed that the interaction of aptamers with heavy metal and other divalent ions proceeds according to different mechanisms, and the aptamers used undergo different conformational changes.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Artyushenko P. V., Mironov V. A., Morozov D. I., Shchugoreva I. A., Borbone N., Tomilin F. N., Kichkailo A. S.
Заглавие : Computational approach to design of aptamers to the receptor binding domain of sars-cov-2
Место публикации : Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P.66-67. - ISSN 18199496 (ISSN), DOI 10.20333/2500136-2021-2-66-67; Сиб. мед. обозрение
Примечания : Cited References: 5
Аннотация: The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, the only one aptamer (Apt16) was selected from the library as a starting aptamer to the RBD protein. For Apt16/RBD complex, molecular dynamic and quantum chemical calculations revealed the pairs of nucleotides and amino acids whose contribution to the binding between aptamer and RBD is the largest. Taking into account these data, Apt16 was subjected to the structure modifications in order to increase the binding with the RBD. Thus, a new aptamer Apt25 was designed. The procedure of 1) aptamer structure modeling/modification, 2) molecular docking, 3) molecular dynamic simulations, 4) quantum chemical calculations was performed sev-eral times. As a result, four aptamers (Apt16, Apt25, Apt27, Apt31) to the RBD were designed in silico without any preliminary experimental data. Binding of the each modeled aptamer to the RBD was studied in terms of interactions between residues in protein and nucleotides in the aptamers. Based on the simulation results, the strongest binding with the RBD was predicted for two Apt27 and Apt31aptamers. The calculated results are in good agreement with experimental data obtained by flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods. Conclusion. The proposed computational approach to selection and refinement of aptamers is universal and can be used for wide range of molecular ligands and targets.
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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Sokolov A. Е., Zabluda V. N., Sherepa A. V., Knyazev Yu. V., Volochaev M. N., Kurilina A., Velikanov D. A., Goncharova D. A., Shabalina A., Svetlichnyi V.
Заглавие : Magnetic properties of iron oxide nanoparticles to create aptamer bionanoconjugates
Коллективы : Aptamers in Russia, international conference
Место публикации : Aptamers in Russia, international conference (1 ; 2019 ; Aug. 27-30 ; Krasnoyarsk). Molecular Therapy - Nucleic Acids: book of abstracts of the 1st Int. conf. "Aptamers in Russia 2019". - 2019. - Vol. 17, Suppl. 1. - P.12
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kostyukov A. S., Isaev I. L., Ershov A. E., Gerasimov V. S., Polyutov S. P., Karpov S. V.
Заглавие : Part II. Nanobubbles around plasmonic nanoparticles in terms of modern simulation modeling: what makes them kill the malignant cells?
Коллективы : Ministry of Science and High Education of Russian Federation [FSRZ-2020-0008]; RFBRRussian Foundation for Basic Research (RFBR); Krasnoyarsk Territory and Krasnoyarsk Regional Fund of Science [20-42-240003]
Место публикации : J. Phys. D. - 2022. - Vol. 55, Is. 17. - Ст.175402. - ISSN 0022-3727, DOI 10.1088/1361-6463/ac4c1f. - ISSN 1361-6463(eISSN)
Примечания : Cited References: 49. - The research was supported by the Ministry of Science and High Education of Russian Federation (Project No. FSRZ-2020-0008), and was funded by RFBR, Krasnoyarsk Territory and Krasnoyarsk Regional Fund of Science, Project No. 20-42-240003
Предметные рубрики: STRESS WAVES
LASER
MEMBRANE
DAMAGE
DEATH
LYSIS
Аннотация: We have established numerically the physical pattern and conditions for formation of nanosized bubbles in aqueous medium around biocompatible plasmonic nanoparticles (NPs) selectively bound to the membrane of the malignant cells by means of DNA-aptamers under the action of picosecond laser radiation. The results obtained are based on the finite volume method and hydrodynamic models underlying the ANSYS Fluent package with extended capabilities. We have found the main features and previously unknown dominant factors of the damage effect on the cell membrane at the moment of the bubble nucleation around the plasmonic NPs of different types taking into account the influence of the closely located membrane. Information on the kinetics of spatial distribution of pressure, temperature and the relative proportion of vapor in the 'nanoparticle-membrane-medium' system have been obtained. The attention is drawn to the advantages of using biocompatible, perfectly absorbing core–shell plasmonic NPs for anti-tumor therapy characterized by an increased mechanical effect on malignant cell membranes at lower laser radiation intensity and the spectral position of their plasmon resonance (λ = 700 nm) in the hemoglobin transparency range. This ensures penetration of laser radiation deep into tissues. The paper is provided with an extensive review of key publications and the state-of-art in this area.
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10.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Stolyar S. V., Li O. A., Nikolaeva E. D., Vorotynov A. M., Velikanov D. A., Knyazev Yu. V., Bayukov O. A., Iskhakov R. S., Kryukova O. V., Pyankov V. F., Volochaev M. N., Mokhov A. A.
Заглавие : Preparation and properties of magnetic composites γ-Fe2O3/SiO2/aptamer(FAS9) for magnetic resonance hyperthermia
Колич.характеристики :8 с
Место публикации : Phys. Met. Metallogr. - 2023. - Vol. 124, Is. 14. - P.1689-1696. - ISSN 0031918X (ISSN), DOI 10.1134/S0031918X23601439. - ISSN 15556190 (eISSN)
Примечания : Cited References: 27
Аннотация: Powders of maghemite γ-Fe2O3 with an average diameter of 8 nm, γ-Fe2O3/SiO2 composites with an agglomerate diameter of about 50 nm and a size of interspersed γ-Fe2O3 particles of 6 nm, and γ‑Fe2O3/SiO2/aptamer(FAS9) composites were synthesized by chemical deposition. Mössbauer spectra were measured, the static and dynamic magnetic properties of the powders were studied, and the coercive force was determined, which decreases from 14 Oe for γ-Fe2O3 powders to 3 Oe for the γ-Fe2O3/SiO2 composite. It is shown that the particle blocking temperature is close to room temperature. The increment of temperature of the powders was measured in the ferromagnetic resonance mode; the temperature of the Fe2O3/SiO2 composite (ΔT ≈ 16°C) turned out to be higher than that of the pure γ-Fe2O3 powder (ΔT ≈ 10°C). It has been experimentally shown that temperature increment ΔT is proportional to the square of the microwave field amplitude. It has been shown that the composition γ-Fe2O3/SiO2/aptamer FAS9 is able to effectively bind to tumor cells, and FMR hyperthermia leads to a decrease in the viability of tumor cells.
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