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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Poolsup S., Zaripov E., Huttmann N., Minic Z., Artyushenko P. V., Shchugoreva I. A., Tomilin F. N., Kichkailo A. S., Berezovski M. V.
Заглавие : Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics
Место публикации : Mol. Ther. Nucleic Acids. - 2023. - Vol. 31. - P.731-743. - ISSN 21622531 (eISSN), DOI 10.1016/j.omtn.2023.02.010
Примечания : Cited References: 74. - M.V.B. thanks the Canadian Institutes of Health Research grant OV1-170353 for providing financial support. Molecular modeling and docking were supported by a grant from the Russian Science Foundation (project number 21-73-20240) for A.S.K. S.P. is thankful to Dr. Bob Dass, Dylan Tanner, and Dr. Degang Liu, Sartorius for generously providing excellent technical training and consumable support for binding assay on BLI, and Aldo Jordan for assisting with creating the figures. The authors also thank John L. Holmes’s mass spectrometry facility for providing access to perform nLC-MS/MS. Lastly, the authors thank the JCSS Joint Super Computer Center of the Russian Academy of Sciences for providing supercomputers for computer simulations
Аннотация: The spread of COVID-19 has affected billions of people across the globe, and the diagnosis of viral infection still needs improvement. Because of high immunogenicity and abundant expression during viral infection, SARS-CoV-2 nucleocapsid (N) protein could be an important diagnostic marker. This study aimed to develop a label-free optical aptasensor fabricated with a novel single-stranded DNA aptamer to detect the N protein. The N-binding aptamers selected using asymmetric-emulsion PCR-SELEX and their binding affinity and cross-reactivity were characterized by biolayer interferometry. The tNSP3 aptamer (44 nt) was identified to bind the N protein of wild type and Delta and Omicron variants with high affinity (KD in the range of 0.6–3.5 nM). Utilizing tNSP3 to detect the N protein spiked in human saliva evinced the potential of this aptamer with a limit of detection of 4.5 nM. Mass spectrometry analysis was performed along with molecular dynamics simulation to obtain an insight into how tNSP3 binds to the N protein. The identified epitope peptides are localized within the RNA-binding domain and C terminus of the N protein. Hence, we confirmed the performance of this aptamer as an analytical tool for COVID-19 diagnosis.
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Вид документа : Статья из журнала
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Автор(ы) : Zamay, Tatiana, Zamay, Sergey, Luzan, Natalia, Fedotovskaya, Victoriya, Masyugin, Albert, Zelenov F., Koshmanova, Anastasia, Nikolaeva, Elena, Kirichenko, Daria, Veprintsev, Dmitry, Kolovskaya, Olga, Shchugoreva, Irina, Zamay, Galina, Lapin I. N., Lukyanenko A. V., Borus, Andrey, Sukhachev A. L., Volochaev M. N., Lukyanenko, Kirill, Shabanov, Alexandr, Zabluda V. N., Zhizhchenko, Alexey, Kuchmizhak, Aleksandr, Sokolov A. Е., Narodov, Andrey, Prokopenko, Vladimir, Galeev, Rinat, Svetlichnyi, Valery, Kichkailo, Anna
Заглавие : Magnetic nanoscalpel for the effective treatment of ascites tumors
Место публикации : J. Funct. Biomater. - 2023. - Vol. 14, Is. 4. - Ст.179. - ISSN 20794983 (eISSN), DOI 10.3390/jfb14040179
Примечания : Cited References: 36. - This research was funded by the Regional State Autonomous Institution “Krasnoyarsk Regional Fund for Support of Scientific and Scientific and Technical Activities”, Competition of scientific, technical, and innovative projects in the interests of the first world-class climate scientific and educational center “Yenisei Siberia”, grant “Carrying out applied research and development aimed at creating technologies for the production of nanoscalpels based on magnetic nanodisks for microsurgery of glial brain tumors” No. 2022060108781 and with the support of a partner company JSC «NPP «Radiosviaz»
Аннотация: One of the promising novel methods for radical tumor resection at a single-cell level is magneto-mechanical microsurgery (MMM) with magnetic nano- or microdisks modified with cancer-recognizing molecules. A low-frequency alternating magnetic field (AMF) remotely drives and controls the procedure. Here, we present characterization and application of magnetic nanodisks (MNDs) as a surgical instrument (“smart nanoscalpel”) at a single-cell level. MNDs with a quasi-dipole three-layer structure (Au/Ni/Au) and DNA aptamer AS42 (AS42-MNDs) on the surface converted magnetic moment into mechanical and destroyed tumor cells. The effectiveness of MMM was analyzed on Ehrlich ascites carcinoma (EAC) cells in vitro and in vivo using sine and square-shaped AMF with frequencies from 1 to 50 Hz with 0.1 to 1 duty-cycle parameters. MMM with the “Nanoscalpel” in a sine-shaped 20 Hz AMF, a rectangular-shaped 10 Hz AMF, and a 0.5 duty cycle was the most effective. A sine-shaped field caused apoptosis, whereas a rectangular-shaped field caused necrosis. Four sessions of MMM with AS42-MNDs significantly reduced the number of cells in the tumor. In contrast, ascites tumors continued to grow in groups of mice and mice treated with MNDs with nonspecific oligonucleotide NO-MND. Thus, applying a “smart nanoscalpel” is practical for the microsurgery of malignant neoplasms.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kichkailo A. S., Narodov A. A., Komarova M. A., Zamay T. N., Zamay G. S., Kolovskaya O. S., Erakhtin E. E., Glazyrin Y. E., Veprintsev D. V., Moryachkov R. V., Zabluda V. N., Shchugoreva I., Artyushenko P., Mironov V. A., Morozov D. I., Gorbushin A. V., Khorzhevskii V. A., Koshmanova A. A., Nikolaeva E. D., Grinev I. P., Voronkovskii I. I., Grek D. S., Belugin K. V., Volzhentsev A. A., Badmaev O. N., Luzan N., Lukyanenko K. A., Peters G., Lapin I. N., Kirichenko A. K., Konarev P. V., Morozov E. V, Mironov G. G., Gargaun A., Muharemagic D., Zamay S. S., Kochkina E. V., Dymova M. A., Smolyarova T. E., Sokolov A. Е., Modestov A. A., Tokarev N. A., Shepelevich N., Ozerskaya A. V., Chanchikova N. G., Krat A. V., Zukov R. A., Bakhtina V. I., Shnyakin P. G., Shesternya P. A., Svetlichnyi V. A., Petrova M. M., Artyukhov I. P., Tomilin F. N., Berezovski, Maxim V.
Заглавие : Development of DNA aptamers for visualization of glial brain tumors and detection of circulating tumor cells
Место публикации : Mol. Ther. - Nucleic Acids. - 2023. - Vol. 32. - P.267-288. - ISSN 21622531 (eISSN), DOI 10.1016/j.omtn.2023.03.015
Примечания : Cited References: 69. - The authors are grateful to all the patients and hospital staff participating in this research. We acknowledge the assistance of the AptamerLab LCC (www.aptamerlab.com) and personally Mr. Vasily Mezko for the aptamer 3D structure optimization and financial and technical support. The authors thank Mr. Alexey Kichkailo, Dr. Arkady B. Kogan, and Dr. Rinat G. Galeev for their general support. Mrs. Valentina L. Grigoreva, and Irina V. Gildebrand for the help with histological staining. Technical and instrumental support was provided by the Multiple-Access Center at Tomsk State University; the Krasnoyarsk Inter-District Ambulance Hospital, named after N.S. Karpovich; John L. Holmes Mass Spectrometry Facility at the University of Ottawa; Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency; Shared Core Facilities of Molecular and Cell Technologies at Krasnoyarsk State Medical University and Krasnoyarsk Regional Centre for Collective Use at the Federal Research Centre “KSC SB RAS”. The confocal fluorescence microscopy research was carried out with the equipment of the Tomsk Regional Core Shared Research Facilities Center of the National Research Tomsk State University. The Center was supported by the Ministry of Science and Higher Education of the Russian Federation, grant no. 075-15-2021-693 (no. 13.RFC.21.0012). Acute toxicity studies were performed in a laboratory certified for preclinical studies, Laboratory of Biological Testing, Institute of Bioorganic Chemistry named after academics M.M. Shemyakin and Y.A. Ovchinnikov Russian Academy of Sciences. The authors are grateful to the Joint Super Computer Center of the Russian Academy of Sciences for providing supercomputers for computer simulations. Development of the glioma tumor model in immunosuppressed mice was supported by the Russian Science Foundation grant No. 22-64-00041 (M.A.D.), https://rscf.ru/en/project/22-64-00041/. Synthesis of 11C-aptamer and PET/CT visualization was funded by the Federal Medical Biological Agency; project 122041800132-2 (A.V.O.). Aptamer selection and their clinical applications were funded by the Ministry of Healthcare of the Russian Federation; project АААА-Б19-219090690032-5 (T.N.Z.). The Ministry of Science and Higher Education of the Russian Federation project FWES-2022-0005 (A.S.K.) supported aptamer characterization, molecular modelling, and in vivo experiments. Mass spectrometry analyses, DNA sequencing, and synthesis were supported by NSERC Discovery Grant (M.V.B.). We acknowledge the European Synchrotron Radiation Facility for SAXS experiments and thank Dr. Bart Van Laer for assistance in using a beamline BM29. SAXS measurements were supported by RFBR № 18-32-00478 for young scientists (R.V.M.). The synchrotron SEC-SAXS data for Gli-55 aptamer were also collected at beamline P12 operated by EMBL Hamburg at the PETRA III storage ring (DESY, Hamburg, Germany)
Аннотация: Here, we present DNA aptamers capable of specific binding to glial tumor cells in vitro, ex vivo, and in vivo for visualization diagnostics of central nervous system tumors. We selected the aptamers binding specifically to the postoperative human glial primary tumors and not to the healthy brain cells and meningioma, using a modified process of systematic evolution of ligands by exponential enrichment to cells; sequenced and analyzed ssDNA pools using bioinformatic tools and identified the best aptamers by their binding abilities; determined three-dimensional structures of lead aptamers (Gli-55 and Gli-233) with small-angle X-ray scattering and molecular modeling; isolated and identified molecular target proteins of the aptamers by mass spectrometry; the potential binding sites of Gli-233 to the target protein and the role of post-translational modifications were verified by molecular dynamics simulations. The anti-glioma aptamers Gli-233 and Gli-55 were used to detect circulating tumor cells in liquid biopsies. These aptamers were used for in situ, ex vivo tissue staining, histopathological analyses, and fluorescence-guided tumor and PET/CT tumor visualization in mice with xenotransplanted human astrocytoma. The aptamers did not show in vivo toxicity in the preclinical animal study. This study demonstrates the potential applications of aptamers for precise diagnostics and fluorescence-guided surgery of brain tumors.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Stolyar S. V., Komogortsev S. V., Gorbenko A. S., Knyazev Yu. V., Yaroslavtsev R. N., Olkhovskiy I. A., Neznakhin D. S., Tyumentseva A. V., Bayukov O. A., Iskhakov R. S.
Заглавие : Maghemite nanoparticles for DNA extraction: Performance and blocking temperature
Место публикации : J. Supercond. Novel Magn. - 2022. - Vol. 35, Is. 7. - P.1929-1936. - ISSN 15571939 (ISSN), DOI 10.1007/s10948-022-06233-5
Примечания : Cited References: 33. - This work was supported by Russian Foundation for Basic Research, Government of Krasnoyarsk Territory, Krasnoyarsk Region Science and Technology Support Fund, with research projects no. 20–42-242902. We are grateful to the Center of Collective Use of FRC KSC SB RAS for the provided equipment
Аннотация: Iron oxide nanoparticles coated with polyethylene glycol were synthesized by coprecipitation for use in the magnetic separation of DNA (deoxyribonucleic acid). The blocking temperature of nanoparticles was studied by the methods of Mossbauer spectroscopy, ferromagnetic resonance, and using magnetometric measurements. The blocking temperature calculated from the temperature dependence of the coercive force was ~ 200 K. The calculation of the blocking temperature from the relaxation time obtained using Mossbauer spectroscopy gave a value of ~ 450 K. The blocking temperature obtained using ferromagnetic resonance was ~ 910 K. The relationship between the obtained blocking temperatures is in good agreement with the Neel-Brown formula. The constants of effective and surface anisotropy were determined by the method of ferromagnetic resonance. Isolation of DNA from blood using prepared particles and separation in a permanent magnet field revealed sufficient productivity, high speed, and the “chemical delicacy” of this approach.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Nikolaeva P. A., Moryachkov R. V., Raldugina V. N., Naumova Iu. O., Novikova T. M., Spiridonova V. A.
Заглавие : Structural analysis of thrombin-binding G-aptamers in presence of bivalent ions
Место публикации : Sib. Med. Rev. - 2022. - Is. 5. - P.111-113. - ISSN 18199496 (ISSN), DOI 10.20333/25000136-2022-5-111-113; Сиб. мед. обозрение
Примечания : Cited References: 4. - The study was supported by a grant from the Russian Science Foundation (project number 21-73-20240)
Аннотация: The aim of this study was to examine 3D structures of DNA aptamers, thrombin inhibitors. The main objective was to study 3D structure 15TBA, RE31, NU172 aptamers using the small-angle X-ray scattering method. The size of 15TBA was 4.5 nm, which corresponds to a partially unfolded conformation. The CD spectrum of Nu172 in the presence of 50 mM strontium ions indicates the presence of an antiparallel G-quadruplex, the concentration o f which drops at 50°C. NU172 does not have a rigid structure, apparently due to the presence of a guanine residue in the GT loop. The NU172 aptamer does not form a stable conformation in solution either without ions or with Ba2+ and Sr2+ ions. It was shown that there is possibility of aptamers transition from one conformation to another dependently on concentration and temperature confirms that the potassium ion is a unique stabilizing ion of natural molecules containing G-quadruplexes.
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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 сборника (однотомник)
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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 журнала
Шифр издания :
Автор(ы) : Moryachkov R. V., Nikolaeva P. A., Spiridonova V. A.
Заглавие : Structure approaches to study of DNA aptamers in solution
Место публикации : Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P.76-78. - ISSN 18199496 (ISSN), DOI 10.20333/2500136-2021-2-76-78; Сиб. мед. обозрение
Примечания : Cited References: 5. - The reported study was funded by RFBR, project number 19-32-90266
Аннотация: The high potential of aptamers – specific molecular agents based on short single-stranded nucleic acids – makes high demands on the molecules under development for the efficiency of interaction with target biomolecules. In this work, approaches are considered for studying the spatial structure of DNA aptamers in solution using various complementary methods, which make it possible to obtain a more complete picture of the formation of the structure and conformational changes, to track the interaction with the target protein, the tendency to oligomerization, and to characterize the spatial structure of both individual molecules and complexes.
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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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10.

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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