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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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Silica-coated iron oxide nanoparticles for DNA isolation for molecular genetic studies in hematology / A. V. Tyumentseva, R. N. Yaroslavtsev, S. V. Stolyar [et al.] // Genet. Test. Mol. Biomark. - 2021. - Vol. 25, Is. 9. - P. 611-614, DOI 10.1089/gtmb.2021.0067. - Cited References: 16 . - ISSN 1945-0265. - ISSN 1945-0257

РУБ Biochemistry & Molecular Biology + Genetics & Heredity
Рубрики:
OXIDATIVE STRESS
MUTATION
DAMAGE
Кл.слова (ненормированные):
magnetic nanoparticles -- DNA isolation -- myeloproliferative neoplasms -- JAK2 V617F
Аннотация: Aim: To develop magnetic nanoparticles (MNPs) based on iron oxide for DNA isolation from blood cells for quantitative molecular genetic analyses of the V617F mutation in the Januskinase 2 (JAK2) gene. Materials and Methods: MNPs were synthesized by the coprecipitation method and coated with tetraethyl orthosilicate (TEOS). The size and shape of the complexes were estimated using transmission electron microscopy. Twenty blood samples from patients with myeloproliferative disorders were used for DNA isolation with the MNPs. DNA quality and compatibility for molecular genetic studies of the JAK2 V617F mutation were investigated by gel electrophoresis and real-time polymerase chain reaction (RT-PCR). Results: The average amount of DNA isolated from 150 μL of whole blood was 75.2 ng when MNPs were used and 72.5 ng when standard silica sorbent was used. There was no DNA damage observed after interaction with MNPs. RT-PCR demonstrated similar values for the JAK2 V617F mutant DNA ratios in the samples after DNA isolation with MNPs and by standard sorption on silica. Conclusions: MNPs with silicate capsules of sufficient thickness were obtained and the undesirable damaging effect of iron oxides on nucleic acids during isolation from cells were eliminated. Designed MNPs allow obtaining intact DNA for molecular genetic studies using the example of the JAK2 V617F for study.

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Держатели документа:
RAS, Krasnoyarsk Sci Ctr, Fed Res Ctr, Siberian Branch, Akademgorodok 50,Str 12-2, Krasnoyarsk 660036, Russia.
Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk, Russia.
Siberian Fed Univ, Krasnoyarsk, Russia.
Fed Med Biol Agcy, Fed Siberian Res Clin Ctr, Fed State Financed Inst, Krasnoyarsk, Russia.
Natl Res Ctr Hematol, Dept Hlth, Krasnoyarsk Branch, Krasnoyarsk, Russia.

Доп.точки доступа:
Tyumentseva, Anna, V; Yaroslavtsev, R. N.; Ярославцев, Роман Николаевич; Stolyar, S. V.; Столяр, Сергей Викторович; Saitova, Alina T.; Саитова, Алина Тимуровна; Tyutrina, Ekaterina S.; Gorbenko, Alexey S.; Stolyar, Marina A.; Olkhovskiy, Igor A.
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Iron oxide nanoparticles for isolating DNA from blood cells / A. V. Tyumentseva, A. S. Gorbenko, R. N. Yaroslavtsev [et al.] // Bull. Russ. Acad. Sci. Phys. - 2021. - Vol. 85, Is. 9. - P. 965-969, DOI 10.3103/S1062873821090185. - Cited References: 13. - This work was supported by the Russian Foundation for Basic Research; the Government of Krasnoyarsk Territory; the Krasnoyarsk Regional Fund for the Support of Scientific and Scientific and Technical Activities, project no. 20-42-242902; and the RF Presidential Council of Grants for the State Support of Young Russian Scientists (Candidates of Science), project no. MK-1263.2020.3 . - ISSN 1062-8738
Кл.слова (ненормированные):
Blood -- Cells -- Cytology -- Iron oxides -- Metal nanoparticles -- Nanomagnetics -- Silicates -- Synthesis (chemical) -- Blood cells -- Cell-be -- Cell/B.E -- Cell/BE -- Leucocytes -- Magnetic iron-oxide nanoparticles -- Physical and chemical properties -- Silicate coatings -- Synthesised -- DNA
Аннотация: Magnetic iron oxide nanoparticles for separating DNA from blood cells are synthesized. Magnetic nanoparticles with a silicate coating are obtained, and their physical and chemical properties are studied. The possibility of using the nanocomposites to isolate DNA from leukocytes for hematological studies is confirmed experimentally.

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Публикация на русском языке Наночастицы оксидов железа для выделения ДНК из клеток крови [Текст] / А. В. Тюменцева, А. С. Горбенко, Р. Н. Ярославцев [и др.] // Изв. РАН. Сер. физич. - 2021. - Т. 85 № 9. - С. 1257-1262

Держатели документа:
Krasnoyarsk Science Center, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation
Hematological Scientific Center, RF Ministry of Health and Social Development, Krasnoyarsk Branch, Krasnoyarsk, 660036, Russian Federation
Kirensky Institute of Physics, Krasnoyarsk Science Center, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, Krasnoyarsk, 660041, Russian Federation

Доп.точки доступа:
Tyumentseva, A. V.; Gorbenko, A. S.; Yaroslavtsev, R. N.; Ярославцев, Роман Николаевич; Stolyar, S. V.; Столяр, Сергей Викторович; Gerasimova, Yu. V.; Герасимова, Юлия Валентиновна; Komogortsev, S. V.; Комогорцев, Сергей Викторович; Bayukov, O. A.; Баюков, Олег Артемьевич; Knyazev, Yu. V.; Князев, Юрий Владимирович; Volochaev, M. N.; Волочаев, Михаил Николаевич; Olkhovskiy, I. A.; Iskhakov, R. S.; Исхаков, Рауф Садыкович
}
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    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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Magnetic Nanoparticles for Extracting DNA from Blood Cells / A. V. Komina, R. N. Yaroslavtsev, Y. V. Gerasimova [et al.] // Bull. Russ. Acad. Sci. Phys. - 2020. - Vol. 84, Is. 11. - P. 1362-1365, DOI 10.3103/S1062873820110155. - Cited References: 15 . - ISSN 1062-8738
Кл.слова (ненормированные):
Blood cells -- Extraction process -- Genomic DNA -- Iron nanoparticles -- Magnetic particle
Аннотация: A technique for extracting DNA from blood cells using magnetic particles offers the advantage of saving time and prospects of automating the extraction process. A way of obtaining magnetic iron nanoparticles for extracting DNA from blood cells is developed. Magnetic nanoparticles with characteristics suitable for extracting genomic DNA from leukocytes are obtained and investigated.

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Публикация на русском языке Магнитные частицы для выделения ДНК из клеток крови [Текст] / А. В. Комина, Р. Н. Ярославцев, Ю. В. Герасимова [и др.] // Изв. РАН. Сер. физич. - 2020. - Т. 84 № 11. - С. 1597-1600

Держатели документа:
Krasnoyarsk Scientific Center, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation
National Research Center for Hematology, Krasnoyarsk Branch, Krasnoyarsk, 660036, Russian Federation
Kirensky Institute of Physics, Krasnoyarsk Scientific Center, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation
Astrakhan State University, Astrakhan, 414056, Russian Federation
Al-Qasim Green University, College of Biotechnology, Babylon, 00964, Iraq

Доп.точки доступа:
Komina, A. V.; Yaroslavtsev, R. N.; Ярославцев, Роман Николаевич; Gerasimova, Yu. V.; Герасимова, Юлия Валентиновна; Stolyar, S. V.; Столяр, Сергей Викторович; Olkhovsky, I. A.; Bairmani, M. S.
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Moryachkov, R. V.
Structure approaches to study of DNA aptamers in solution / R. V. Moryachkov, P. A. Nikolaeva, V. A. Spiridonova // Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P. 76-78 ; Сиб. мед. обозрение, DOI 10.20333/2500136-2021-2-76-78. - Cited References: 5. - The reported study was funded by RFBR, project number 19-32-90266 . - ISSN 1819-9496
Кл.слова (ненормированные):
biomolecules in solution -- tertiary structure -- small-angle X-ray scattering (SAXS) -- structure analysis
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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Держатели документа:
Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50, Akademgorodok St., Krasnoyarsk, 660036, Russian Federation
Kirensky Institute of Physics, Bld. 38, 50, Akademgorodok St., Krasnoyarsk, 660036, Russian Federation
Lomonosov Moscow State University, 1, Leninskie Gory St., Moscow, 119992, Russian Federation
A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Bld. 40, 1, Leninskie Gory St., Moscow, 119992, Russian Federation

Доп.точки доступа:
Nikolaeva, P. A.; Spiridonova, V. A.; Морячков, Роман Владимирович

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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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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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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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Magnetic nanoscalpel for the effective treatment of ascites tumors / T. Zamay, S. Zamay, N. Luzan [et al.] // J. Funct. Biomater. - 2023. - Vol. 14, Is. 4. - Ст. 179, DOI 10.3390/jfb14040179. - 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» . - ISSN 2079-4983
Кл.слова (ненормированные):
magnetic nanodisks -- ascitic tumor -- magneto-mechanical therapy -- “smart nanoscalpel” -- DNA aptamers -- apoptosis -- necrosis
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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Держатели документа:
Federal Research Center “Krasnoyarsk Science Center” of the Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
JSC «NPP «Radiosviaz», Krasnoyarsk 660021, Russia
Laboratory of Advanced Materials and Technology, Siberian Physical Technical Institute, Tomsk State University, Tomsk 634050, Russia
L.V. Kirensky Institute of Physics, Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
Institute of Automation and Control Processes (IACP), Far Eastern Branch of the Russian Academy of Science, Vladivostok 690041, Russia
Far Eastern Federal University, Vladivostok 690950, Russia
V.P. Astafiev Krasnoyarsk State Pedagogical University, Krasnoyarsk 660049, Russia

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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.; Лукьяненко, Анна Витальевна; Borus, Andrey; Борус, Андрей Андреевич; Sukhachev, A. L.; Сухачев, Александр Леонидович; Volochaev, M. N.; Волочаев, Михаил Николаевич; Lukyanenko, Kirill; Shabanov, Alexandr; Zabluda, V. N.; Заблуда, Владимир Николаевич; Zhizhchenko, Alexey; Kuchmizhak, Aleksandr; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Narodov, Andrey; Prokopenko, Vladimir; Galeev, Rinat; Svetlichnyi, Valery; Kichkailo, Anna
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10.

Development of DNA aptamers for visualization of glial brain tumors and detection of circulating tumor cells / A. S. Kichkailo, A. A. Narodov, M. A. Komarova [et al.] // Mol. Ther. - Nucleic Acids. - 2023. - Vol. 32. - P. 267-288, DOI 10.1016/j.omtn.2023.03.015. - 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) . - ISSN 2162-2531
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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Держатели документа:
Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
Department of Molecular Electronics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 50 Akademgorodok, Krasnoyarsk 660036, Russia
National Research Center Kurchatov Institute, 1 Akademika Kurchatova, Moscow 123182, Russia
Laboratory of Advanced Materials and Technology, Siberian Physical-Technical Institute of Tomsk State University, 36 Lenina, Tomsk 634050, Russia
Krasnoyarsk Regional Pathology-Anatomic Bureau, 3d Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie gory, Moscow 119991, Russia
Department of Chemistry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 702-701, South Korea
Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland
A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” RAS, 59 Leninsky pr., Moscow, 119333, Russia
Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
Krasnoyarsk Regional Clinical Cancer Center, 16 1-ya Smolenskaya, Krasnoyarsk 660133, 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
Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, Ontario K1N6N5, Canada
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 8 Lavrentyev Avenue, 630090 Novosibirsk, Russia

Доп.точки доступа:
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.; Заблуда, Владимир Николаевич; 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.; Лапин, И. Н.; 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.; Соколов, Алексей Эдуардович; 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.; Томилин, Феликс Николаевич; Berezovski, Maxim V.
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