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Characterizing aptamer interaction with the oncolytic virus VV-GMCSF-Lact / M. A. Dymova, D. O. Malysheva, V. K. Popova [et al.] // Molecules. - 2024. - Vol. 29, Is. 4. - Ст. 848, DOI 10.3390/molecules29040848. - Cited References: 46. - This study was supported by the Russian Science Foundation grant No. 22-64-00041, available online: https://rscf.ru/en/project/22-64-00041/ (accessed on 6 February 2024). This work was supported by the Russian state-funded project for ICBFM SB RAS (grant number 121030200173-6) . - ISSN 1420-3049
Кл.слова (ненормированные):
aptamer -- oncolytic virus -- glioma -- dynamic light scattering -- microscale thermophoresis
Аннотация: Aptamers are currently being investigated for their potential to improve virotherapy. They offer several advantages, including the ability to prevent the aggregation of viral particles, enhance target specificity, and protect against the neutralizing effects of antibodies. The purpose of this study was to comprehensively investigate an aptamer capable of enhancing virotherapy. This involved characterizing the previously selected aptamer for vaccinia virus (VACV), evaluating the aggregation and molecular interaction of the optimized aptamers with the recombinant oncolytic virus VV-GMCSF-Lact, and estimating their immunoshielding properties in the presence of human blood serum. We chose one optimized aptamer, NV14t_56, with the highest affinity to the virus from the pool of several truncated aptamers and built its 3D model. The NV14t_56 remained stable in human blood serum for 1 h and bound to VV-GMCSF-Lact in the micromolar range (Kd ≈ 0.35 μM). Based on dynamic light scattering data, it has been demonstrated that aptamers surround viral particles and inhibit aggregate formation. In the presence of serum, the hydrodynamic diameter (by intensity) of the aptamer–virus complex did not change. Microscale thermophoresis (MST) experiments showed that NV14t_56 binds with virus (EC50 = 1.487 × 109 PFU/mL). The analysis of the amplitudes of MST curves reveals that the components of the serum bind to the aptamer–virus complex without disrupting it. In vitro experiments demonstrated the efficacy of VV-GMCSF-Lact in conjunction with the aptamer when exposed to human blood serum in the absence of neutralizing antibodies (Nabs). Thus, NV14t_56 has the ability to inhibit virus aggregation, allowing VV-GMCSF-Lact to maintain its effectiveness throughout the storage period and subsequent use. When employing aptamers as protective agents for oncolytic viruses, the presence of neutralizing antibodies should be taken into account.

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Держатели документа:
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev av. 8, 630090 Novosibirsk, Russia
Department of Natural Sciences, Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
State Research Center of Virology and Biotechnology “Vector”, 630559 Koltsovo, Russia
Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, Partizana Zheleznyaka str. 1, 660022 Krasnoyarsk, Russia
Federal Research Center KSC SB RAS, 50 Akademgorodok, 660036 Krasnoyarsk, Russia
Kirensky Institute of Physics, 50/38 Akademgorodok, 660012 Krasnoyarsk, Russia

Доп.точки доступа:
Dymova, M. A.; Malysheva, D. O.; Popova, V. K.; Dmitrienko, E. V.; Endutkin, A. V.; Drokov, D. V.; Mukhanov, V. S.; Byvakina, A. A.; Kochneva, G. V.; Artyushenko, P. V.; Shchugoreva, I. A.; Rogova, A. V.; Tomilin, F. N.; Томилин, Феликс Николаевич; Kichkailo, A. S.; Richter, V. A.; Kuligina, E. V.
}
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Bioluminescent aptamer-based microassay for detection of melanoma inhibitory activity protein (MIA) / E. E. Bashmakova, A. N. Kudryavtsev, A. E. Tupikin [et al.] // Anal. Methods. - 2024, DOI 10.1039/D4AY00706A. - Cited References: 23 . - Article in press. - ISSN 1759-9660. - ISSN 1759-9679
Аннотация: Melanoma inhibitory activity protein (MIA) does obviously offer the potential to reveal clinical manifestations of melanoma. Despite a pressing need for effective diagnosis of this highly fatal disease, there are no clinically approved MIA detection ELISA kits available. A recommended MIA threshold has not yet been defined, mostly by reason of variability in immunoglobulins' affinity and stability, the difference in sample preparation and assay conditions. Here we present a pair of high-affinity DNA aptamers developed as an alternative recognition and binding element for MIA detection. Their stability and reproducible synthesis are expected to ensure this analysis under standard conditions. The devised aptamer-based solid-phase microassay of model standard and control human sera involves luciferase NLuc as a highly sensitive reporter. Bioluminescence dependence on MIA concentration ranges in a linear manner from 2.5 to 250 ng mL−1, providing a MIA detection limit of 1.67 ± 0.57 ng mL−1.

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Держатели документа:
Institute of Biophysics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia
Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
Kirensky Institute of Physics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia
Siberian Federal University, Krasnoyarsk, Russia

Доп.точки доступа:
Bashmakova, E. E.; Kudryavtsev, A. N.; Tupikin, A. E.; Kabilov, M. R.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Frank, L. A.
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Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics / S. Poolsup, E. Zaripov, N. Huttmann [et al.] // Mol. Ther. Nucleic Acids. - 2023. - Vol. 31. - P. 731-743, DOI 10.1016/j.omtn.2023.02.010. - 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 . - ISSN 2162-2531
Кл.слова (ненормированные):
MT: Oligonucleotides: Diagnostics and Biosensors -- COVID-19 diagnosis -- SARS-CoV-2 nucleocapsid detection -- label-free optical aptasensor -- aptamer selection -- biolayer interferometry -- binding motif identification
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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Держатели документа:
Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk 660036, Russia
Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia
Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk 660036, Russia

Доп.точки доступа:
Poolsup, S.; Zaripov, E.; Huttmann, N.; Minic, Z.; Artyushenko, P. V.; Shchugoreva, I. A.; Tomilin, F. N.; Томилин, Феликс Николаевич; Kichkailo, A. S.; Berezovski, M. V.
}
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Towards understanding the triggering of the malignant cell death in high-efficiency magneto-mechanical anticancer therapy / P. N. Semina, I. L. Isaev, S. K. Komogortsev [et al.] // J. Phys. D. - 2023. - Vol. 56, Is. 6. - Ст. 065401, DOI 10.1088/1361-6463/acb0dd. - Cited References: 146. - P N S, A S K, D E K, S P P, S V K acknowledge the support by the Ministry of Science and High Education of Russian Federation (Project No. FSRZ-2020-0008). Experimental analyses were funded by the Ministry of Science and Higher Education of the Russian Federation (Project FWES-2022-0005) – A S K, T N Z. The authors thank Dr S V Saikova for providing the TEM image in figure (b) . - ISSN 0022-3727. - ISSN 1361-6463
Кл.слова (ненормированные):
magnetic nanoparticle -- malignant cell membrane -- apoptosis -- anticancer therapy -- aptamer
Аннотация: The paper discusses schemes for the implementation of magneto-mechanical anticancer therapy and the most probable scenarios of damaging mechanical eﬀects on the membranes of malignant cells by targeted magnetic nanoparticles selectively bound to membrane mechanoreceptors employing aptamers. The conditions for selective triggering of the malignant cell apoptosis in a low-frequency non-heating alternating magnetic ﬁeld, corresponding to the exceeding threshold value of the force acting on the membrane and its mechanoreceptors, are established using a nanoparticle dynamic simulation. The requirements for the functionality of magnetic nanoparticles and their suitability for biomedical applications are analysed. Attention is paid to the possibility of the formation of magnetite nanoparticle aggregates in an external magnetic ﬁeld and their localization near tumor cell membranes. It is shown that the scenario involving the process of aggregation of magnetite nanoparticles provides a suﬃcient magneto-mechanical impact to achieve a therapeutic eﬀect. A possible explanation for the experimentally established fact of successful application of magneto-mechanical therapy using magnetite nanoparticles is presented, in which complete suppression of the Ehrlich carcinoma in an alternating magnetic ﬁeld as a response to a magnetome-chanical stimulus was demonstrated. This result conﬁrmed the possibility of using the method for high eﬃciency treatment of malignant neoplasms. The paper is provided with an extensive review of key publications and the state of art in this area.

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Держатели документа:
International Research Center of Spectroscopy and Quantum Chemistry—IRC SQC, Siberian Federal University, Krasnoyarsk 660041, Russia
Institute of Computational Modelling of the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
L. V. Kirensky Institute of Physics, Federal Research Center KSC the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
Federal Research Center "Krasnoyarsk Science Center" of the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
Siberian Federal University, Krasnoyarsk 660041, Russia
Tomsk State University, Tomsk 634050, Russia
Federal Siberian Research Clinical Center, Federal Medical Biological Agency of Russian Federation, Krasnoyarsk 660037, Russia

Доп.точки доступа:
Semina, P. N.; Семина, Полина Николаевна; Isaev, I. L.; Исаев, Иван Леонидович; Komogortsev, S. V.; Комогорцев, Сергей Викторович; Klyuchantsev, A. B.; Ключанцев, А. Б.; Kostyukov, A. S.; Blagodatova, A. V.; Khrennikov, D. E.; Kichkailo, A. S.; Кичкайло, Анна Сергеевна; Zamay, T. N.; Замай, Т. Н.; Lapin, I. N.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Polyutov, S. P.; Полютов, Сергей Петрович; Karpov, S. V.; Карпов, Сергей Васильевич
}
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Monitoring of breast cancer progression via aptamer-based detection of circulating tumor cells in clinical blood samples / O. S. Kolovskaya, A. V. Zyuzyukina, J. P. Dassie [et al.] // Front. Mol. Biosci. - 2023. - Vol. 10. - Ст. 1184285, DOI 10.3389/fmolb.2023.1184285. - Cited References: 37. - CTCs isolation method development and clinical sample analyses were supported by the Ministry of Healthcare of Russian Federation project REYC-2023-0012. The Ministry of Science and Higher Education of the Russian Federation project FWES-2022-0005 supported aptamer characterization, molecular modeling. MDA-231/LUC cells were from R. Domann (Jenkin et al. Breast Cancer Research, 2005). Technical and instrumental support was provided by the 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). - 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 Vasily Mezko for the technical support. The authors thank Valentina L. Grigoreva, and Irina V. Gildebrand for the help with СTC staining . - ISSN 2296-889X
Аннотация: Introduction: Breast cancer (BC) diagnostics lack noninvasive methods and procedures for screening and monitoring disease dynamics. Admitted CellSearch® is used for fluid biopsy and capture of circulating tumor cells of only epithelial origin. Here we describe an RNA aptamer (MDA231) for detecting BC cells in clinical samples, including blood. The MDA231 aptamer was originally selected against triple-negative breast cancer cell line MDA-MB-231 using cell-SELEX. Methods: The aptamer structure in solution was predicted using mFold program and molecular dynamic simulations. The affinity and specificity of the evolved aptamers were evaluated by flow cytometry and laser scanning microscopy on clinical tissues from breast cancer patients. CTCs were isolated form the patients’ blood using the developed method of aptamer-based magnetic separation. Breast cancer origin of CTCs was confirmed by cytological, RT-qPCR and Immunocytochemical analyses. Results: MDA231 can specifically recognize breast cancer cells in surgically resected tissues from patients with different molecular subtypes: triple-negative, Luminal A, and Luminal B, but not in benign tumors, lung cancer, glial tumor and healthy epithelial from lungs and breast. This RNA aptamer can identify cancer cells in complex cellular environments, including tumor biopsies (e.g., tumor tissues vs. margins) and clinical blood samples (e.g., circulating tumor cells). Breast cancer origin of the aptamer-based magnetically separated CTCs has been proved by immunocytochemistry and mammaglobin mRNA expression. Discussion: We suggest a simple, minimally-invasive breast cancer diagnostic method based on non-epithelial MDA231 aptamer-specific magnetic isolation of circulating tumor cells. Isolated cells are intact and can be utilized for molecular diagnostics purposes.

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Держатели документа:
Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
Department of Oncology and Radiation Therapy, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
Krasnoyarsk Regional Clinical Cancer Center Named After A.I. Kryzhanovsky, Krasnoyarsk, Russia
Department of Internal Medicine, University of Iowa, Iowa, IA, United States
Department of General Surgery, Named After Prof. M.I. Gulman, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
Department of Pathological Anatomy, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
Krasnoyarsk Regional Pathology-Anatomic Bureau, Krasnoyarsk, Russia
Laboratory of Advanced Materials and Technology, Siberian Physical Technical Institute, Tomsk State University, Tomsk, Russia
School of Non-Ferrous Metals and Materials Science, Siberian Federal University, Krasnoyarsk, Russia
Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk, Russia
Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
Russian Scientific Center of Roentgenoradiology, Moscow, Russia
Alferov Federal State Budgetary Institution of Higher Education and Science, Saint Petersburg National Research Academic University of the Russian Academy of Sciences, Saint Petersburg, Russia
Institute for Analytical Instrumentation of the Russian Academy of Sciences, Saint Petersburg, Russia
Platform Discovery Sciences, Biology, Wave Life Sciences, Cambridge, MA, United States

Доп.точки доступа:
Kolovskaya, Olga S.; Zyuzyukina, Alena V.; Dassie, Justin P.; Zamay, Galina S.; Zamay, Tatiana N.; Boyakova, Nina V.; Khorzhevskii, Vladimir A.; Kirichenko, Daria A.; Lapin, I. N.; Лапин, И. Н.; Shchugoreva, Irina A.; Artyushenko, Polina V.; Tomilin, F. N.; Томилин, Феликс Николаевич; Veprintsev, Dmitry V.; Glazyrin, Yury E.; Minic, Zoran; Bozhenko, Vladimir K.; Kudinova, Elena A.; Kiseleva, Yana Y.; Krat, Alexey V.; Slepov, Eugene V.; Bukatin, Anton S.; Zukov, Ruslan A.; Shesternya, Pavel A.; Berezovski, Maxim V.; Giangrande, Paloma H.; Kichkailo, Anna S.
}
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Preparation and properties of magnetic composites γ-Fe2O3/SiO2/aptamer(FAS9) for magnetic resonance hyperthermia / S. V. Stolyar, O. A. Li, E. D. Nikolaeva [et al.] // Phys. Met. Metallogr. - 2023. - Vol. 124, Is. 14. - P. 1689-1696, DOI 10.1134/S0031918X23601439. - Cited References: 27 . - ISSN 0031-918X. - ISSN 1555-6190
Кл.слова (ненормированные):
ferromagnetic resonance -- magnetic hyperthermia -- maghemite
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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Держатели документа:
Federal Research Center, Krasnoyarsk Science Center, Siberian Branch of the Russian Academy of Sciences, 660036, Krasnoyarsk, Russia
Siberian Federal University, 660041, Krasnoyarsk, Russia
Kirensky Institute of Physics, Federal Research Center KSC, Siberian Branch Russian Academy of Sciences, 660036, Krasnoyarsk, Russia

Доп.точки доступа:
Stolyar, S. V.; Столяр, Сергей Викторович; Li, O. A.; Nikolaeva, E. D.; Vorotynov, A. M.; Воротынов, Александр Михайлович; Velikanov, D. A.; Великанов, Дмитрий Анатольевич; Knyazev, Yu. V.; Князев, Юрий Владимирович; Bayukov, O. A.; Баюков, Олег Артемьевич; Iskhakov, R. S.; Исхаков, Рауф Садыкович; Kryukova, O. V.; Pyankov, V. F.; Volochaev, M. N.; Волочаев, Михаил Николаевич; Mokhov, A. A.
}
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Aptamer modified Au/Ni/Au nanodiscs for magnetomechanical cell surgery / A. Е. Sokolov, A. V. Lukyanenko, V. N. Zabluda [et al.] // V International Baltic Conference on Magnetism. IBCM : Book of abstracts. - 2023. - P. 12. - Cited References: 3

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Держатели документа:
Kirensky Institute of Physics, Federal Research Center KSC SB RAS
Krasnoyarsk State Medical University
Federal Research Center KSC SB RAS

Доп.точки доступа:
Sokolov, A. Е.; Соколов, Алексей Эдуардович; Lukyanenko, A. V.; Лукьяненко, Анна Витальевна; Zabluda, V. N.; Заблуда, Владимир Николаевич; Borus, A. A.; Борус, Андрей Андреевич; Zamay, G. S.; Замай, Галина Сергеевна; Zamay, T. N.; Luzan, N.; Zamay, S. S.; International Baltic Conference on Magnetism(5 ; 2023 ; Aug. 20-24 ; Svetlogorsk, Russia); Балтийский федеральный университет им. И. Канта
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    Part II. Nanobubbles around plasmonic nanoparticles in terms of modern simulation modeling: what makes them kill the malignant cells? / A. S. Kostyukov, I. L. Isaev, A. E. Ershov [et al.] // J. Phys. D. - 2022. - Vol. 55, Is. 17. - Ст. 175402, DOI 10.1088/1361-6463/ac4c1f. - 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 . - ISSN 0022-3727. - ISSN 1361-6463
   Перевод заглавия: Часть II. Нанопузырьки вокруг плазмонных наночастиц с точки зрения современного имитационного моделирования: что заставляет их убивать злокачественные клетки?

РУБ Physics, Applied
Рубрики:
STRESS WAVES
   LASER
   MEMBRANE
   DAMAGE
   DEATH
   LYSIS
Кл.слова (ненормированные):
photothermal effect -- plasmonic nanoparticle -- malignant cell membrane -- pulsed laser radiation -- finite elements analysis -- anticancer therapy -- aptamer
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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Держатели документа:
Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem IRC SQC, Krasnoyarsk 660041, Russia.
Russian Acad Sci, Inst Computat Modelling, Siberian Branch, Krasnoyarsk 660036, Russia.
Fed Med Biol Agcy Russian Federat, Fed Siberian Res Clin Ctr, Krasnoyarsk 660037, Russia.
Russian Acad Sci, LV Kirensky Inst Phys, Fed Res Ctr KSC, Siberian Branch, Krasnoyarsk 660036, Russia.

Доп.точки доступа:
Kostyukov, A. S.; Isaev, I. L.; Ershov, A. E.; Gerasimov, V. S.; Polyutov, S. P.; Karpov, S. V.; Карпов, Сергей Васильевич; 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]
}
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Nucleic acid aptamers increase the anticancer efficiency and reduce the toxicity of cisplatin-arabinogalactan conjugates in vivo / T. N. Zamay, A. K. Starkov, O. S. Kolovskaya [et al.] // Nucleic Acid Ther. - 2022. - Vol. 32, Is. 6. - P. 497-506, DOI 10.1089/nat.2022.0024. - Cited References: 42 . - ISSN 2159-3337. - ISSN 2159-3345
Кл.слова (ненормированные):
cisplatin -- aptamer -- arabinogalactan -- cancer chemotherapy -- ascites carcinoma
Аннотация: Cisplatin is an effective drug for treating various cancer types. However, it is highly toxic for both healthy and tumor cells. Therefore, there is a need to reduce its therapeutic dose and increase targeted bioavailability. One of the ways to achieve this could be the coating of cisplatin with polysaccharides and specific carriers for targeted delivery. Nucleic acid aptamers could be used as carriers for the specific delivery of medicine to cancer cells. Cisplatin-arabinogalactan-aptamer (Cis-AG-Ap) conjugate was synthesized based on Cis-dichlorodiammineplatinum, Siberian larch arabinogalactan, and aptamer AS-42 specific to heat-shock proteins (HSP) 71?kDa (Hspa8) and HSP 90-beta (Hsp90ab1). The antitumor effect was estimated using ascites and metastatic Ehrlich tumor models. Cis-AG-Ap toxicity was assessed by blood biochemistry on healthy mice. Here, we demonstrated enhanced anticancer activity of Cis-AG-Ap and its specific accumulation in tumor foci. It was shown that targeted delivery allowed a 15-fold reduction in the therapeutic dose of cisplatin and its toxicity. Cis-AG-Ap sufficiently suppressed the growth of Ehrlich's ascites carcinoma, the mass and extent of tumor metastasis in vivo. Arabinogalactan and the aptamers promoted cisplatin efficiency by enhancing its bioavailability. The described strategy could be very promising for targeted anticancer therapy.

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Держатели документа:
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russian Federation
Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russian Federation
Institute of Chemistry and Chemical Technology SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS, Krasnoyarsk660036, Russian Federation
Department of Chemistry, Siberian Federal University, Krasnoyarsk, Russian Federation
Laboratory for Physics of Magnetic Phenomena, Kirensky Institute of Physics, Federal Research Center Krasnoyarsk Science Center SB RAS, Krasnoyarsk, Russian Federation
Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada

Доп.точки доступа:
Zamay, T. N.; Starkov, A. K.; Kolovskaya, O. S.; Zamay, G. S.; Veprintsev, D. V.; Luzan, N.; Nikolaeva, E. D.; Lukyanenko, K. A.; Artyushenko, P. V.; Shchugoreva, I. A.; Glazyrin, Y. E.; Koshmanova, A. A.; Krat, A. V.; Tereshina, D. S.; Zamay, S. S.; Pats, Y. S.; Zukov, R. A.; Tomilin, F. N.; Томилин, Феликс Николаевич; Berezovski, M. V.; Kichkailo, A. S.
}
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10.

Applying joint theoretical experimental research to aptamer modeling / I. A. Shchugoreva, P. V. Artyushenko, F. N. Tomilin [et al.] // Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P. 105-106 ; Сиб. мед. обозрение, DOI 10.20333/2500136-2021-2-105-106. - Cited References: 4 . - ISSN 1819-9496
Кл.слова (ненормированные):
LC-18 -- DNA aptamer -- lung adenocarcinoma -- SAXS -- DFTB3
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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Держатели документа:
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, 660036, Russian Federation
Department of Chemistry, Siberian Federal University, Krasnoyarsk, 660041, Russian Federation
Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk, 660012, Russian Federation
Nanoscience Center and Department of Chemistry, University of Jyvaskyla, Jyvaskyla, 40014, Finland
Department of Chemistry, Lomonosov Moscow State University, Moscow, 119234, Russian Federation

Доп.точки доступа:
Shchugoreva, I. A.; Artyushenko, P. V.; Tomilin, F. N.; Morozov, D. I.; Mironov, V. A.; Moryachkov, R. V.; Морячков, Роман Владимирович; Kichkailo, A. S.

}
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11.

Computational approach to design of aptamers to the receptor binding domain of sars-cov-2 / P. V. Artyushenko, V. A. Mironov, D. I. Morozov [et al.] // Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P. 66-67 ; Сиб. мед. обозрение, DOI 10.20333/2500136-2021-2-66-67. - Cited References: 5 . - ISSN 1819-9496
Кл.слова (ненормированные):
selection -- aptamer -- receptor-binding domain -- SARS-CoV-2
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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Держатели документа:
Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, Krasnoyarsk, 660041, Russian Federation
Lomonosov Moscow State University, Moscow, 119991, Russian Federation
University of Jyvaskyla, Jyvaskyla, 40014, Finland
University of Naples Federico II, Naples, 80138, Italy
Kirensky Institute of Physics KSC SB RAS, Krasnoyarsk, 660036, Russian Federation

Доп.точки доступа:
Artyushenko, P. V.; Mironov, V. A.; Morozov, D. I.; Shchugoreva, I. A.; Borbone, N.; Tomilin, F. N.; Томилин, Феликс Николаевич; Kichkailo, A. S.

}
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12.

    The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer / D. Morozov, V. Mironov, R. V. Moryachkov [et al.] // Mol. Ther. Nucl. Acids. - 2021. - Vol. 25. - P. 316-327, DOI 10.1016/j.omtn.2021.07.015. - 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 . - ISSN 2162-2531
   Перевод заглавия: Роль малоуглового рентгеновского рассеяния и молекулярного моделирования в выснении трёхмерной структуры ДНК аптамера против рака лёгкого
Кл.слова (ненормированные):
aptamer -- oligonucleotide -- tertiary structure -- spatial structure -- lung adenocarcinoma -- small-angle X-ray scattering -- SAXS -- molecular dynamics -- fragment molecular orbital -- molecular simulations
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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Держатели документа:
Nanoscience Center and Department of Chemistry, University of Jyvaskyla, P.O. Box 35, Jyvaskyla, 40014, Finland
Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk, 660022, Russian Federation
Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk, 660041, Russian Federation
European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8568, Japan
Computational Science Division, Argonne National Laboratory, Lemont, IL, United States

Доп.точки доступа:
Morozov, D.; Mironov, V.; Moryachkov, R. V.; Морячков, Роман Владимирович; Shchugoreva, I. A.; Artyushenko, P. V.; Zamay, G. S.; Kolovskaya, O. S.; Zamay, T. N.; Krat, A. V.; Molodenskiy, D. S.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Veprintsev, D. V.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Zukov, R. A.; Berezovski, M. V.; Tomilin, F. N.; Томилин, Феликс Николаевич; Fedorov, D. G.; Alexeev, Y.; Kichkailo, A. S.
}
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13.

11C-radiolabeled aptamer for imaging of tumors and metastases using positron emission tomography-computed tomography / A. V. Ozerskaya, T. N. Zamay, O. S. Kolovskaya [et al.] // Mol. Ther. Nucl. Acids. - 2021. - Vol. 26. - P. 1159-1172, DOI 10.1016/j.omtn.2021.10.020. - Cited References: 44 . - ISSN 2162-2531
Кл.слова (ненормированные):
11C radiolabeling -- radiopharmaceuticals -- PET/CT -- in vivo imaging -- DNA aptamers -- Ehrlich ascites carcinoma -- metastasis
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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Держатели документа:
Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russian Federation
Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russian Federation
Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russian Federation
Kirensky Institute of Physics, Krasnoyarsk, Russian Federation
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
Krasnoyarsk Regional Pathology-Anatomic Bureau, Krasnoyarsk, Russian Federation

Доп.точки доступа:
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.; Морячков, Роман Владимирович; Zabluda, V. N.; Заблуда, Владимир Николаевич; 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.; Смолярова, Татьяна Евгеньевна; Tomilin, F. N.; Томилин, Феликс Николаевич; Zamay, S. S.; Silnikov, V. N.; Berezovski, M. V.; Kichkailo, A. S.
}
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14.

The role of small-angle X-ray scattering and molecular simulations in 3D structure elucidation of a DNA aptamer-cancer cells magnetic separation agent / R. V. Moryachkov, D. Morozov, V. Mironov [et al.] // 4th International Baltic Conference on Magnetism (IBCM 2021) : Book of abstracts. - 2021. - P. 168. - Cited References: 2. - The reported study was funded by RFBR, project number 19-32-90266

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Держатели документа:
Kirensky Institute of Physics, Federal Research Center KSC SB RAS

Доп.точки доступа:
Moryachkov, R. V.; Морячков, Роман Владимирович; Morozov, D.; Mironov, V.; Shchugoreva, I.; Artyushenko, P. V.; Артюшенко, Полина Владимировна; Zamay, G. S.; Замай Г. С.; Molodenskiy, D. S.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Kichkailo, A.S.; Кичкайло, Анна Сергеевна; Sokolov, A. Е.; Соколов, Алексей Эдуардович; International Baltic Conference on Magnetism: focus on nanobiomedicine and smart materials(4 ; 2021 ; Aug. 29-Sept. 2 ; Svetlogorsk, Russia); Балтийский федеральный университет им. И. Канта
}
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15.

The Ca2+-regulated photoprotein obelin as a tool for SELEX monitoring and DNA aptamer affinity evaluation / V. V. Krasitskaya, N. S. Goncharova, V. V. Biriukov [et al.] // Photochem. Photobiol. - 2020. - Vol. 96, Is. 5. - P. 1041-1046, DOI 10.1111/php.13274. - Cited References: 25. - This work has been supported by the Russian Foundation for Basic Research (RFBR) under the grant no 18-38-00531. . - ISSN 0031-8655. - ISSN 1751-1097

РУБ Biochemistry & Molecular Biology + Biophysics
Рубрики:
CARDIAC TROPONIN-I
   BIOLUMINESCENCE
   IMMUNOASSAY
   APTASENSOR
   DIAGNOSIS
Аннотация: Bioluminescent solid-phase analysis was proposed to monitor the selection process and to determine binding characteristics of the aptamer-target complexes during design and development of the specific aptamers. The assay involves Ca2+-regulated photoprotein obelin as a simple, sensitive and fast reporter. Applicability and the prospects of the approach were exemplified by identification of DNA aptamers to cardiac troponin I, a highly specific early biomarker for acute myocardial infarction. Two structurally different aptamers specific to various epitopes of troponin I were obtained and then tested in a model bioluminescent assay.

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Держатели документа:
Fed Res Ctr KSC SB RAS, Inst Biophys SB RAS, Krasnoyarsk, Russia.
Siberian Fed Univ, Krasnoyarsk, Russia.
Inst Chem Biol & Fundamental Med SB RAS, Novosibirsk, Russia.
Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk, Russia.

Доп.точки доступа:
Krasitskaya, V. V.; Goncharova, N. S.; Biriukov, V. V.; Bashmakova, E. E.; Kabilov, M. R.; Baykov, I. K.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Frank, L. A.; Russian Foundation for Basic Research (RFBR)Russian Foundation for Basic Research (RFBR) [18-38-00531]
}
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16.

    Small-angle scattering applications to the analysis of aptamer structure and conformational changes / R. V. Moryachkov, V. N. Zabluda, A. N. Berlina [et al.] // AIP Conference Proceedings : book of abstracts. - 2020. - Vol. 2299. - Ст. 040002 ; Synchrotron and free electron laser radiation: generation and application (SFR-2020). - Novosibirsk. - P. 45-46, DOI 10.1063/5.0030394. - 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
   Перевод заглавия: Использование малоуглового рассеяния для анализа структуры и конформационных изменений аптамеров
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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Держатели документа:
Kirensky Institute of Physics, Akademgorodok 50, bld. 38, Krasnoyarsk, 660012, Russian Federation
Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50, Krasnoyarsk, 660012, Russian Federation
A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation
National Research Center “Kurchatov Institute”, Akademika Kurchatova pl. 1, Moscow, 123182, Russian Federation

Доп.точки доступа:
Moryachkov, R. V.; Морячков, Роман Владимирович; Zabluda, V. N.; Заблуда, Владимир Николаевич; Berlina, A. N.; Peters, G. S.; Kichkailo, A. S.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Internetional Conference on Synchrotron and Free Electron Laser Radiation: Generation and Application(2020 ; 13-16 July ; Novosibirsk)

}
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17.

Molecular epitope determination of aptamer complexes of the multidomain protein C-met by proteolytic affinity-mass spectrometry / L. Lupu, P. Wiegand, N. Huttmann [et al.] // ChemMedChem. - 2020. - Vol. 15, Is. 4. - P. 363-369, DOI 10.1002/cmdc.201900489. - Cited References: 40. - We gratefully acknowledge the advice and assistance of Prof. Friedemann Volklein and Oliver Muller, MSc in the preparation of chips for the SPR affinity determinations. We thank Dr. Stefan Maeser, Biogen GmbH, Munchen, for valuable advice and critical reading of the manuscript. This work has been partially funded (Chip-MS epitope analysis) by the LOEWE-3 Funding Agency, Hessen-Agentur, Wiesbaden, Germany; Grant 696/19-16 . - ISSN 1860-7179. - ISSN 1860-7187

РУБ Chemistry, Medicinal + Pharmacology & Pharmacy
Рубрики:
DNA APTAMERS
ANTIBODIES
RECOGNITION
Кл.слова (ненормированные):
C-Met protein -- tumor biomarkers -- aptamer-C-Met complexes -- aptamer epitopes -- affinity-mass spectrometry -- epitope peptide analysis
Аннотация: C‐Met protein is a glycosylated receptor tyrosine kinase of the hepatocyte growth factor (HGF), composed of an α and a β chain. Upon ligand binding, C‐Met transmits intracellular signals by a unique multi‐substrate docking site. C‐Met can be aberrantly activated leading to tumorigenesis and other diseases, and has been recognized as a biomarker in cancer diagnosis. C‐Met aptamers have been recently considered a useful tool for detection of cancer biomarkers. Herein we report a molecular interaction study of human C‐Met expressed in kidney cells with two DNA aptamers of 60 and 64 bases (CLN0003 and CLN0004), obtained using the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure. Epitope peptides of aptamer‐C‐Met complexes were identified by proteolytic affinity‐mass spectrometry in combination with SPR biosensor analysis (PROTEX‐SPR‐MS), using high‐pressure proteolysis for efficient digestion. High affinities (KD, 80–510 nM) were determined for aptamer‐C‐Met complexes, with two‐step binding suggested by kinetic analysis. A linear epitope, C‐Met (381–393) was identified for CLN0004, while the CLN0003 aptamer revealed an assembled epitope comprised of two peptide sequences, C‐Met (524–543) and C‐Met (557–568). Structure modeling of C‐Met‐aptamers were consistent with the identified epitopes. Specificities and affinities were ascertained by SPR analysis of the synthetic epitope peptides. The high affinities of aptamers to C‐Met, and the specific epitopes revealed render them of high interest for cellular diagnostic studies.

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Steinbeis Ctr Biopolymer Anal & Biomed Mass Spect, Marktstr 29, D-65428 Russelsheim, Germany.
Univ Ottawa, Dept Chem & Biomol Sci, Ottawa, ON K1N 6N5, Canada.
Rhein Main Univ, Dept Engn Sci, D-65428 Russelsheim, Germany.
Russian Acad Sci, Siberian Branch, Kirensky Inst Phys, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Krasnoyarsk 66041, Russia.
Russian Acad Sci, Fed Res Ctr, Lab Digital Controlled Drugs & Theranost, Siberian Branch,Krasnoyarsk Sci Ctr, Krasnoyarsk 660036, Russia.
Pressure Biosci Inc, 14 Norfolk Ave, South Easton, MA 02375 USA.

Доп.точки доступа:
Lupu, Loredana; Wiegand, Pascal; Huttmann, N.; Rawer, Stephan; Kleinekofort, Wolfgang; Shugureva, Irina; Kichkailo, Anna S.; Tomilin, F. N.; Томилин, Феликс Николаевич; Lazarev, Alexander; Berezovski, Maxim V.; Przybylski, Michael; LOEWE-3 Funding Agency, Hessen-Agentur, Wiesbaden, Germany [696/19-16]
}
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18.

Aptamer-conjugated superparamagnetic ferroarabinogalactan nanoparticles for targeted magnetodynamic therapy of cancer / O. S. Kolovskaya, T. N. Zamay, G. S. Zamay [et al.] // Cancers. - 2020. - Vol. 12, Is. 1. - Ст. 216, DOI 10.3390/cancers12010216. - Cited References: 46. - This research was funded by the Ministry of Science and Higher Education of the Russian Federation; project 0287-2019-0007 . - ISSN 2072-6694
Кл.слова (ненормированные):
aptamers -- arabinogalactan -- superparamagnetic ferroarabinogalactans -- drug delivery -- magnetodynamic therapy -- magnetically induced cell disruption -- magnetic resonance imaging
Аннотация: Nanotechnologies involving physical methods of tumor destruction using functional oligonucleotides are promising for targeted cancer therapy. Our study presents magnetodynamic therapy for selective elimination of tumor cells in vivo using DNA aptamer-functionalized magnetic nanoparticles exposed to a low frequency alternating magnetic field. We developed an enhanced targeting approach of cancer cells with aptamers and arabinogalactan. Aptamers to fibronectin (AS-14) and heat shock cognate 71 kDa protein (AS-42) facilitated the delivery of the nanoparticles to Ehrlich carcinoma cells, and arabinogalactan (AG) promoted internalization through asialoglycoprotein receptors. Specific delivery of the aptamer-modified FeAG nanoparticles to the tumor site was confirmed by magnetic resonance imaging (MRI). After the following treatment with a low frequency alternating magnetic field, AS-FeAG caused cancer cell death in vitro and tumor reduction in vivo. Histological analyses showed mechanical disruption of tumor tissues, total necrosis, cell lysis, and disruption of the extracellular matrix. The enhanced targeted magnetic theranostics with the aptamer conjugated superparamagnetic ferroarabinogalactans opens up a new venue for making biocompatible contrasting agents for MRI imaging and performing non-invasive anti-cancer therapies with a deep penetrated magnetic field.

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Держатели документа:
Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, 660036 Krasnoyarsk, Russia
Laboratory for Biomolecular and Medical Technologies, Faculty of Medicine, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, 660022 Krasnoyarsk, Russia
Irkutsk Institute of Chemistry named after A.E. Favorsky, the Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
L.V. Kirensky Institute of Physics SB RAS—The Branch of Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 660036 Krasnoyarsk, Russia
Laboratory of Advanced Materials and Technology, Tomsk State University, 634050 Tomsk, Russia
Institute of Chemistry and Chemical Technology SB RAS—The Branch of Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 660036 Krasnoyarsk, Russia
School of Engineering Physics and Radio Electronics, Siberian Federal University, 660041 Krasnoyarsk, Russia
Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
School of Non-Ferrous Metals and Materials Science, Siberian Federal University, 660041 Krasnoyarsk, Russia
Faculty of Physics, Department of Magnetism, Lomonosov Moscow State University, 119991 Moscow, Russia
School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada

Доп.точки доступа:
Kolovskaya, O. S.; Коловская, О. С.; Zamay, T. N.; Замай, Т. Н.; Zamay, G. S.; Замай, Галина Сергеевна; Babkin, V. A.; Medvedeva, E. N.; Neverova, N. A.; Kirichenko, A. K.; Zamay, S. S.; Замай, С. С.; Lapin, I. N.; Morozov, E. V.; Морозов, Евгений Владимирович; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Narodov, A. A.; Fedorov, D. G.; Tomilin, F. N.; Томилин, Феликс Николаевич; Zabluda, V. N.; Заблуда, Владимир Николаевич; Alekhina, Yu.; Lukyanenko, K. A.; Glazyrin, Yu. E.; Svetlichnyi, V. A.; Berezovski, M. V.; Kichkailo, A. S.
}
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19.

Electrochemical Study of Sensor with Aptamer Specific to Glioblastoma / D. O. Sharko [et al.] // 20th International Conference of Young Specialists on Micro/Nanotechnologies and Electron Devices, EDM 2019 : (29 June 2019 through 3 July 2019; Erlagol, Altai Republic, Russian Federation) : IEEE Computer Society, 2019. - Vol. 2019-June. - Ст. 8823563. - P. 612-615, DOI 10.1109/EDM.2019.8823563. - Cited References: 10. - The work is supported by the Grant of the President of the Russian Federation (MK-5284.2018.3).
Кл.слова (ненормированные):
aptamer -- electrochemical sensor -- glioblastoma
Аннотация: An aptasensor consisting of a gold disc electrode and aptamer Gli-233 specific to glioblastoma was prepared with different methods and studied by electrochemical and microscopic methods. It was found, that the real electro active surface area and electric double layer capacitance changed with the electrode modification. The highest capacitance was registered for the electrode modified with the simultaneous immobilization of Gli-233 and additional blocking agent (mercaptoethanol). It was shown that to develop an impedimetric sensor on the basis of Gli-233, it is necessary to optimize the conditions for the signal registration.

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Держатели документа:
Siberian Physical-Technical Institute, Tomsk State University, Tomsk, Russian Federation
Voino-Jasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russian Federation
Kirensky Institute of Physics, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Sharko, D. O.; Shabalina, A. V.; Gotovtseva, E. Y.; Zamay, G. S.; Замай, Г. С.; Zamay, S. S.; Замай, С. С.; International Conference of Young Specialists on Micro/Nanotechnologies and Electron Devices(20 ; 2019 ; Jun.-Jul. ; Erlagol, Altai Republic)
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20.

Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation / F. N. Tomilin [et al.] // Anal. Bioanal. Chem. - 2019. - Vol. 411, Is. 25. - P. 6723-6732, DOI 10.1007/s00216-019-02045-0. - Cited References: 51. - Authors are grateful to Ana Gargaun for English grammar correction. This work was funded in parts by the Ministry of Science and Higher Education of the Russian Federation; project 0287-2019-0007 the Council of the President of the Russian Federation for Support of Young Scientists and Leading Scientific Schools (project no. SP-938.2015.5) and the grant of KSAI “Krasnoyarsk Regional Fund of Supporting Scientific and Technological Activities” for M.P., the internship “The study of the stacking of the secondary structure of DNA aptamers to thrombin” for R.M. . - ISSN 1618-2642
Кл.слова (ненормированные):
Aptamer -- Thrombin -- Three-dimensional structure -- Small-angle X-ray scattering -- Molecular modeling
Аннотация: Nucleic acid (NA) aptamers bind to their targets with high affinity and selectivity. The three-dimensional (3D) structures of aptamers play a major role in these non-covalent interactions. Here, we use a four-step approach to determine a true 3D structure of aptamers in solution using small-angle X-ray scattering (SAXS) and molecular structure restoration (MSR). The approach consists of (i) acquiring SAXS experimental data of an aptamer in solution, (ii) building a spatial distribution of the molecule’s electron density using SAXS results, (iii) constructing a 3D model of the aptamer from its nucleotide primary sequence and secondary structure, and (iv) comparing and refining the modeled 3D structures with the experimental SAXS model. In the proof-of-principle we analyzed the 3D structure of RE31 aptamer to thrombin in a native free state at different temperatures and validated it by circular dichroism (CD). The resulting 3D structure of RE31 has the most energetically favorable conformation and the same elements such as a B-form duplex, non-complementary region, and two G-quartets which were previously reported by X-ray diffraction (XRD) from a single crystal. More broadly, this study demonstrates the complementary approach for constructing and adjusting the 3D structures of aptamers, DNAzymes, and ribozymes in solution, and could supply new opportunities for developing functional nucleic acids. [Figure not available: see fulltext.]. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.

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Держатели документа:
Kirensky Institute of Physics, Federal Research Center KSC Siberian Branch Russian Academy of Sciences, 50/38 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, 79 Svobodny pr., Krasnoyarsk, 660041, Russian Federation
Federal Research Center “Krasnoyarsk Science Center” Siberian Branch of the Russian Academy of Sciences, 50 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
NRC Kurchatov Institute, 1, Academic Kurchatov Square, Moscow, 123182, Russian Federation
A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1/40 Leninskie Gory, Moscow, 119992, Russian Federation
Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk, 660022, Russian Federation
Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada

Доп.точки доступа:
Tomilin, F. N.; Томилин, Феликс Николаевич; Moryachkov, R.; Морячков, Роман Владимирович; Shchugoreva, I.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Peters, G.; Platunov, M. S.; Платунов, Михаил Сергеевич; Spiridonova, V.; Melnichuk, A.; Atrokhova, A.; Zamay, S. S.; Замай, С. С.; Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич; Zamay, G. S.; Замай, Галина Сергеевна; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Zamay, T. N.; Замай, Т. Н.; Berezovski, M. V.; Kichkailo, A. S.
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