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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kim P. D., Zamay S. S., Zamay T. N., Prokopenko V. S., Kolovskaya O. S., Zamay G. S., Princ, V. Ya., Seleznev V. A., Komonov A. I., Spivak E. A., Rudenko R. Y., Dubinina A. V., Komarov A. V., Denisenko V. V., Komarova M. A., Sokolov A. E., Narodov A. A., Zjivaev V. P., Zamay A. S.
Заглавие : The antitumor effect of magnetic nanodisks and DNA aptamer conjugates
Коллективы : Russian Science Foundation [14-15-00805]
Место публикации : Dokl. Biochem. Biophys.: MAIK Nauka-Interperiodica / Springer, 2016. - Vol. 466, Is. 1. - P.66-69. - ISSN 1607-6729, DOI 10.1134/S1607672916010154. - ISSN 1608-3091(eISSN)
Примечания : Cited References:7. - This work was supported by the Russian Science Foundation (project no. 14-15-00805).
Предметные рубрики: Nanoparticles
Cells
Аннотация: Here we describe a method of forming large arrays (up to 109 pieces) of free magnetic Ni-nanodisks 50 nm thick coated on both sides with layers of 5 nm thick Au. The antitumor effect of the magnetic nickel gold-coated nanodisks and DNA aptamer conjugates was evaluated in vivo and in vitro. Under the influence of rotating magnetic field, the studied nanodisks can cause the death of Ehrlich ascites carcinoma cells.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Gorban A., Popova T., Zinovyev A.
Заглавие : Codon usage trajectories and 7-cluster structure of 143 complete bacterial genornic sequences
Разночтения заглавия :авие SCOPUS: Codon usage trajectories and 7-cluster structure of 143 complete bacterial genomic sequences
Место публикации : Physica A: ELSEVIER SCIENCE BV, 2005. - Vol. 353. - P365-387. - ISSN 0378-4371, DOI 10.1016/j.physa.2005.01.043
Примечания : Cited References: 46
Предметные рубрики: DNA-BASE COMPOSITION
ASYMMETRIC SUBSTITUTION PATTERNS
PROTEIN-CODING REGIONS
MICROBIAL GENOMES
GENE IDENTIFICATION
MARKOV-MODELS
G+C CONTENT
BIAS
PREDICTION
SELECTION
Ключевые слова (''Своб.индексиров.''): genome--cluster--codon usage--correlations--entropy--mean field--cluster--codon usage--correlations--entropy--genome--mean field--approximation theory--correlation methods--database systems--entropy--functions--genes--mathematical models--clusters--codon usage--genomes--mean field--bacteria
Аннотация: Three results are presented. First, we prove the existence of a universal 7-cluster structure in all 143 completely sequenced bacterial genomes available in Genbank in August 2004, and explained its properties. The 7-cluster structure is responsible for the main part of sequence heterogeneity in bacterial genomes. In this sense, our 7 clusters is the basic model of bacterial genome sequence. We demonstrated that there are four basic "pure" types of this model, observed in nature: "parallel triangles", "perpendicular triangles", degenerated case and the flower-like type. Second, we answered the question: how big are the position-specific information and the contribution connected with correlations between nucleotide. The accuracy of the mean-field (context-free) approximation is estimated for bacterial genomes. We show that codon us-age of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy (more precisely, by two similar functions, one for eubacterial genomes and the other one for archaea). Description of these two codon-usage trajectories is the third result. All 143 cluster animated 3D-scatters are collected in a database and is made available on our web-site: http://www.ihes.fr/similar to zinovyev/7clusters. (c) 2005 Elsevier B.V. All rights reserved.
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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Shchugoreva I., Moryachkov R., Zabluda V. N., Sokolov A. E., Spiridonova V. A., Gruzinov A., Zamay A. S., Veprincev D., Zamay G. S., Tomilin F. N., Ovchinnikov S. G.
Заглавие : Molecular design of aptamer structure by computer simulations
Коллективы : Euro-Asian Symposium "Trends in MAGnetism", "Trends in MAGnetism", Euro-Asian Symposium, Институт физики им. Л.В. Киренского Сибирского отделения РАН
Место публикации : VI Euro-Asian Symposium "Trends in MAGnetism" (EASTMAG-2016): abstracts/ ed.: O. A. Maksimova, R. D. Ivantsov. - Krasnoyarsk: KIP RAS SB, 2016. - Ст.P12.2. - P.558. - ISBN 978-5-904603-06-9 (Шифр -478014040)
Примечания : We acknowledge the grant by the Ministry of Education and Science (Agreement No.14.607.21.0104 (RFMEFI60714X0104)) for the financial support of this work
Ключевые слова (''Своб.индексиров.''): dna--selex--saxs--qm/mm--aptamer--g-quartets
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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Sokolov A. E., Ivanova O. S., Zabluda V. N., Dubynina A. V., Semina P. N., Zamay G. S., Zamay T. N., Zamay A. S., Volochaev M. N., Svetlichnyi V., Lapin I. N., Shabalina A.
Заглавие : Magnetic and magnetooptical properties of magnetic nanoparticles and DNA-Aptamers conjugates for medical application
Коллективы : Euro-Asian Symposium "Trends in MAGnetism", "Trends in MAGnetism", Euro-Asian Symposium, Институт физики им. Л.В. Киренского Сибирского отделения РАН
Место публикации : VI Euro-Asian Symposium "Trends in MAGnetism" (EASTMAG-2016): abstracts/ ed.: O. A. Maksimova, R. D. Ivantsov. - Krasnoyarsk: KIP RAS SB, 2016. - Ст.P12.4. - P.561. - ISBN 978-5-904603-06-9 (Шифр -478014040)
Примечания : The work was supported by the Ministry of Education and Science (Agreement No.14.607.21.0104 (RFMEFI60714X0104))
Ключевые слова (''Своб.индексиров.''): magnetic nanoparticles--magnetization--natural and magnetic circular dichroism--aptamers--bionanoconjugates
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Zamay G. S., Belyanina I. V., Zamay A. S., Komarova M. A., Krat A. V., Eremina E. N., Zukov R. A., Sokolov A. Е., Zamay T. N.
Заглавие : Selection of DNA aptamers for breast cancer
Место публикации : Biochem. Mosc.-Suppl. Ser. B-Biomed. Chem. - 2016. - Vol. 10, Is. 2. - P.158-164. - ISSN 1990-7508, DOI 10.1134/S1990750816020128. - ISSN 1990-7516(eISSN)
Примечания : Cited References:23
Предметные рубрики: BIOMARKERS
MORTALITY
PATTERNS
Ключевые слова (''Своб.индексиров.''): selex--dna aptamers--oligonucleotides--breast cancer
Аннотация: A method of selection of DNA aptamers to breast tumor tissue based on the use of postoperative material has been developed. Breast cancer tissues were used as the positive target; the negative targets included benign tumor tissue, adjacent healthy tissues, breast tissues from mastopathy patients, and also tissues of other types of malignant tumors. During selection a pool of DNA aptamers demonstrating selective binding to breast cancer cells and tissues and insignificant binding to breast benign tissues has been obtained. These DNA aptamers can be used for identification of protein markers, breast cancer diagnostics, and targeted delivery of anticancer drugs.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Gorelik V. S., Zlobina L. I., Krylov A. S., Sverbil V. P., Sverbil P. P.
Заглавие : Raman scattering in dried DNA and crystalline amino acids
Место публикации : Phys. Wave Phenom.: Allerton Press, 2016. - Vol. 24, Is. 4. - P.272-278. - ISSN 1541308X (ISSN), DOI 10.3103/S1541308X1604004X
Примечания : Cited References: 53. - The work was supported in part by the RFBR Projects 14-02-00190 and 16-52-00026 (BRFFR - RFBR F16R-063).
Аннотация: Raman spectrum characteristics of dried deoxyribonucleic acid (DNA) and two types of crystalline amino acids (L-lysine, D-asparagine) are compared in a wide range of frequencies, including the regions of lattice (7 to 200 cm−1) and intramolecular (200 to 4000 cm−1) vibrations. It is found that the spectral position of the low-frequency band in the Raman spectrum of DNA with a peak near 26 cm−1 correlates with the Raman spectrum of high-Q low-frequency modes that manifest themselves in the crystalline amino acids under investigation. The low-frequency band of DNA refers to a twist-like vibrational mode of nucleobases. The intensities of this DNA mode and the high-Q lattice modes of the crystalline amino acids L-lysine and D-asparagine are several times as high as those of the Raman lines corresponding to the intramolecular modes. Resonant coupling of low-frequency modes of DNA and amino acid molecular chains is analyzed. © 2016, Allerton Press, Inc.
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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Sokolov A. Е., Zamay S. S., Zamay T. , Svetlichnyi V., Velikanov D. A.
Заглавие : Magnetic nanoparticles and DNA-aptamers conjugates for diagnostics and therapy of cancer : Invited
Коллективы : Federal Research Center KSC SB RAS, Kirensky Institute of Physics, Siberian Federal Univercity, International Workshop on Actual Problems of Condensed Matter Physics
Место публикации : International workshop on actual problems of condensed matter physics: Program. Book of abstracts/ Fed. Res. Center KSC SB RAS, Kirensky Inst. of phys., Sib. Fed. Univ. - Krasnoyarsk, 2017. - P.13 (Шифр В37/H99-812624296)
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Вид документа : Однотомное издание
Шифр издания :
Заглавие : International workshop on actual problems of condensed matter physics : Program. Book of abstracts
Выходные данные : Krasnoyarsk, 2017
Колич.характеристики :30 с
Коллективы : Federal Research Center KSC SB RAS, Kirensky Institute of Physics, Siberian Federal Univercity, International Workshop on Actual Problems of Condensed Matter Physics (27 Mar. - 1 Apr. 2017; Krasnoyarsk/ Cheremushki) :
Содержание : Magnetic and transport properties of the epitaxial Fe3Si film on a Si substrate/ I. A. Bondarev. The magnetic anisotropy of the Fe and Fe(1-x)Si(x) thin films depend on/ I. A. Yakovlev [и др.]. Inverted opals as the Josephson networks of weak links/ S. I. Popkov [и др.]. Electronic structure and Fermi surface within the cluster perturbation theory in X-operators representation/ S. Nikolaev, V. I. Kuz'min, S. G. Ovchinnikov. DFT investigation of electronic and optical magnetic properties of one dimensional transition metal halide structuresTmHaI3/ A. S. Fedorov [и др.]. Effect of interatomic exchange interaction on spin crossover and Mott-Hubbard transition under high pressure and the physical properties of the low Earth’s mantle/ S. G. Ovchinnikov [и др.]. Extremely high magnetic-field sensitivity of charge transport in the Mn/SiO2/p-Si hybrid structure/ I. A. Tarasov [и др.]. Marnetic-field sensitivity of charge transport in silicon-based hybrid structures/ N. V. Volkov [et al.]. Fabrication of multi-terminal planar devices based on epitaxial Fe1-xSix films grown on Si(111)/ A. V. Lukyanenko, A. S. Tarasov, I. A. Tarasov [et al.] ; A. V. Luyanenko [и др.]. Magnetic field-driven lateral photovoltaic effect in the Fe/SiO2/p-Si hibrid structure with the Scottky barrier/ M. V. Rautskii [и др.]. Small angle X-ray scattering and atomic structure of aptamer biomolecules/ R. Moryachkov [и др.]. Iron silicides and pure iron epitaxial and highly-textured nanostructures on silicon: growth and their physical properties/ I. A. Tarasov [и др.]. Magnetic nanoparticles and DNA-aptamers conjugates for diagnostics and therapy of cancer/ A. E. Sokolov [и др.]. The microscopic origin of ferromagnetism in Fe silicides/ I. S. Sandalov [и др.].
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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Sokolov A. Е., Ivanova O. S., Zabluda V. N., Dubinina A. V., Semina P. N., Zamay G. S., Zamay T. N., Zamay S. S., Volochaev M. N., Svetlichnyi V., Lapin I. N., Shabalina A., Solodova O. V.
Заглавие : Magnetic nanoparticles and DNA-aptamers conjugates for cancer therapy
Коллективы : International Baltic Conference on Magnetism: Focus on funcshionalized magnetic structures for energy and biotechnology , Балтийский федеральный университет им. И. Канта
Место публикации : Int. Baltic Conf. Magnet. (IBCM-2017) : Focus on funcshionalized magnetic struct. for energy and biotech.: book of abstracts. - 2017. - P.77
Примечания : Библиогр.: 4
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10.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Belyanina I. V., Zamay T. N., Zamay G. S., Zamay S. S., Kolovskaya, Olga S., Ivanchenko, Tatiana I., Denisenko, Valery V., Kirichenko, Andrey K., Glazyrin, Yury E., Garanzha, Irina V., Grigorieva, Valentina V., Shabanov A. V., Veprintsev, Dmitry V., Sokolov A. E., Sadovskii, Vladimir M., Gargaun, Ana, Berezovski M. V., Kichkailo, Anna S.
Заглавие : In vivo cancer cells elimination guided by aptamer-functionalized gold-coated magnetic nanoparticles and controlled with low frequency alternating magnetic field
Коллективы : Russian Scientific Fund [14-15-00805]
Место публикации : Theranostics. - 2017. - Vol. 7, Is. 13. - P.3326-3337. - ISSN 1838-7640, DOI 10.7150/thno.17089
Примечания : Cited References:35. - The authors are grateful to George Y. Vorogeikin, Yuri I. Vorogeikin and "OKB ART". Andrey Barinov and "OPTEC Group" for help with 3D laser scanning imaging. Microscopic analyses using Carl Zeiss LSM 800 were done in the "Center for bioassay, nanotechnology and nanomaterials safety" ("Biotest-Nano") (Multiple-Access Center, Tomsk State University, Tomsk, Russia). Toxicity studies have been performed in Multiple-Access Center, Central Scientific Research Laboratory in Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecky. This work was supported by the Russian Scientific Fund (grant #14-15-00805).
Предметные рубрики: PHOTOTHERMAL THERAPY
INTEGRIN ACTIVATION
FIBRONECTIN
STIMULATION
Ключевые слова (''Своб.индексиров.''): cancer therapy--gold coated magnetic nanoparticles--dna aptamers--low--frequency alternating magnetic field--fibronectin--integrin--apoptosis--necrosis
Аннотация: Biomedical applications of magnetic nanoparticles under the influence of a magnetic field have been proved useful beyond expectations in cancer therapy. Magnetic nanoparticles are effective heat mediators, drug nanocarriers, and contrast agents; various strategies have been suggested to selectively target tumor cancer cells. Our study presents magnetodynamic nanotherapy using DNA aptamer-functionalized 50 nm gold-coated magnetic nanoparticles exposed to a low frequency alternating magnetic field for selective elimination of tumor cells in vivo. The cell specific DNA aptamer AS-14 binds to the fibronectin protein in Ehrlich carcinoma hence helps deliver the gold-coated magnetic nanoparticles to the mouse tumor. Applying an alternating magnetic field of 50 Hz at the tumor site causes the nanoparticles to oscillate and pull the fibronectin proteins and integrins to the surface of the cell membrane. This results in apoptosis followed by necrosis of tumor cells without heating the tumor, adjacent healthy cells and tissues. The aptamer-guided nanoparticles and the low frequency alternating magnetic field demonstrates a unique non-invasive nanoscalpel technology for precise cancer surgery at the single cell level.
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11.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Stolyar S. V., Chekanova L. A., Yaroslavtsev R. N., Komogortsev S. V., Gerasimova Yu. V., Bayukov O. A., Volochaev M. N., Iskhakov R. S., Garanzha I. V., Kolovskaya O. S., Bairmani M. Sh., Zamay T. N.
Заглавие : Magnetic nanoconstructions of iron oxides coated with arabinogalactan functionalized with DNA aptamer
Коллективы : International Scientific Conference "Conference on Applied Physics, Information Technologies and Engineering"
Место публикации : J. Phys. Conf. Ser. - 2019. - Vol. 1399. - Ст.022026. - ISSN 1742-6588, DOI 10.1088/1742-6596/1399/2/022026. - ISSN 1742-6596 (eISSN)
Примечания : Cited References: 6
Предметные рубрики: Applied Physics
Аннотация: New composite nanoparticles for biomedical applications have been manufactured. The particles consist of an anisomeric magnetite core coated with arabinogalactan and are functionalized with cameras for As-14 ascites cells (Ehrlich carcinoma). The binding of ascitic Ehrlich carcinoma cells to magnetic nanoparticles was evaluated using fluorescence microscopy.
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12.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Lupu, Loredana, Wiegand, Pascal, Huttmann N., Rawer, Stephan, Kleinekofort, Wolfgang, Shugureva, Irina, Kichkailo, Anna S., Tomilin F. N., Lazarev, Alexander, Berezovski, Maxim V., Przybylski, Michael
Заглавие : Molecular epitope determination of aptamer complexes of the multidomain protein C-met by proteolytic affinity-mass spectrometry
Коллективы : LOEWE-3 Funding Agency, Hessen-Agentur, Wiesbaden, Germany [696/19-16]
Место публикации : ChemMedChem. - 2020. - Vol. 15, Is. 4. - P.363-369. - ISSN 1860-7179, DOI 10.1002/cmdc.201900489. - ISSN 1860-7187(eISSN)
Примечания : 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
Предметные рубрики: DNA APTAMERS
ANTIBODIES
RECOGNITION
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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13.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Krasitskaya V. V., Goncharova N. S., Biriukov V. V., Bashmakova E. E., Kabilov M. R., Baykov I. K., Sokolov A. Е., Frank L. A.
Заглавие : The Ca2+-regulated photoprotein obelin as a tool for SELEX monitoring and DNA aptamer affinity evaluation
Коллективы : Russian Foundation for Basic Research (RFBR)Russian Foundation for Basic Research (RFBR) [18-38-00531]
Место публикации : Photochem. Photobiol. - 2020. - Vol. 96, Is. 5. - P.1041-1046. - ISSN 0031-8655, DOI 10.1111/php.13274. - ISSN 1751-1097(eISSN)
Примечания : Cited References: 25. - This work has been supported by the Russian Foundation for Basic Research (RFBR) under the grant no 18-38-00531.
Предметные 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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14.

Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Sokolov A. Е., Kurilova A. V., Svetlichniy V. A., Velikanov D. A., Sherepa A. V., Volochaev M. N., Goncharova D. A., Shabalina A. V.
Заглавие : Obtaining and properties of biomagnetic nanoconjugates based on DNA aptamers and magnetic nanoparticles for magnetodynamic cell therapy
Коллективы : Asian School-Conference on Physics and Technology of Nanostructured Materials, Азиатская школа-конференция по физике и технологии наноструктурированных материалов
Место публикации : The Fifth Asian School-Conference on Physics and Technology of Nanostructured Materials: Proceedings. - VLadivostok: Dalnauka Publishing, 2020. - Ст.V.01.17o. - P.147. - ISBN 978-5-8044-1698-1
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15.

Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Moryachkov R. V., Berlina A. N., Artyushenko P. V., Zabluda V. N., Peters G. S., Sokolov A. Е.
Заглавие : Conformational changes in DNA aptamers upon binding to Pb ions
Коллективы : Asian School-Conference on Physics and Technology of Nanostructured Materials, Азиатская школа-конференция по физике и технологии наноструктурированных материалов
Место публикации : The Fifth Asian School-Conference on Physics and Technology of Nanostructured Materials: Proceedings. - VLadivostok: Dalnauka Publishing, 2020. - Ст.VII.31.01p. - P.193. - ISBN 978-5-8044-1698-1
Примечания : The reported study was funded by RFBR, project number 19-32-90266.
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16.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Komina A. V., Yaroslavtsev R. N., Gerasimova Yu. V., Stolyar S. V., Olkhovsky I. A., Bairmani M. S.
Заглавие : Magnetic Nanoparticles for Extracting DNA from Blood Cells
Место публикации : Bull. Russ. Acad. Sci. Phys. - 2020. - Vol. 84, Is. 11. - P.1362-1365. - ISSN 10628738 (ISSN), DOI 10.3103/S1062873820110155
Примечания : Cited References: 15
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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17.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Moryachkov R. V., Nikolaeva P. A., Spiridonova V. A.
Заглавие : Structure approaches to study of DNA aptamers in solution
Место публикации : Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P.76-78. - ISSN 18199496 (ISSN), DOI 10.20333/2500136-2021-2-76-78; Сиб. мед. обозрение
Примечания : Cited References: 5. - The reported study was funded by RFBR, project number 19-32-90266
Аннотация: The high potential of aptamers – specific molecular agents based on short single-stranded nucleic acids – makes high demands on the molecules under development for the efficiency of interaction with target biomolecules. In this work, approaches are considered for studying the spatial structure of DNA aptamers in solution using various complementary methods, which make it possible to obtain a more complete picture of the formation of the structure and conformational changes, to track the interaction with the target protein, the tendency to oligomerization, and to characterize the spatial structure of both individual molecules and complexes.
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18.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Shchugoreva I. A., Artyushenko P. V., Tomilin F. N., Morozov D. I., Mironov V. A., Moryachkov R. V., Kichkailo A. S.
Заглавие : Applying joint theoretical experimental research to aptamer modeling
Место публикации : Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P.105-106. - ISSN 18199496 (ISSN), DOI 10.20333/2500136-2021-2-105-106; Сиб. мед. обозрение
Примечания : Cited References: 4
Аннотация: The aim of the research. In this work we studied the structure of LC-18 DNA aptamer, which exhibits specific binding to lung adenocarcinoma cells. Obtain-ing the 3D structure of the aptamer is necessary for understanding the mechanism of binding of the aptamer to the target. Therefore, the aim of the research was modeling of the LC-18 aptamer spatial structure using combination of theoretical methods: DNA folding tools, quantum-chemical calculations and molecular dynamic simulations. Material and methods. The secondary structure of the LC-18 aptamer was predicted by using OligoAnalyzer and MFold online software under the conditions typical small-angle X-ray scattering (SAXS) experiment. The molecular modeling of the aptamer was carried out using the Avogadro program. For prediction of the structure two computational methods were used: quantum-mechanical method with third-order density-functional tight-binding (DFTB3) and molecular dynamics (MD) with force fields. Results. In this paper it was shown that molecular simulations can predict structures from the SAXS experiments. OligoAnalyzer and MFold web servers have been used to generate a set of several likely models. However, more accurate calculations have showed that these models do not predict the relative importance of isomers. Meanwhile, application of quantum-chemical and molecular dynamics calculations have showed reliable molecular structures which have a small deviations from the experimental SAXS curves. Conclusion. This study demonstrates the approach for modeling 3D structures of DNA-aptamers in solution using both experimental and theoretical meth-ods. It could be very helpful in designing more efficient aptamers based on results obtained from molecular simulations.
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19.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Morozov D., Mironov V., Moryachkov R. V., Shchugoreva I. A., Artyushenko P. V., Zamay G. S., Kolovskaya O. S., Zamay T. N., Krat A. V., Molodenskiy D. S., Zabluda V. N., Veprintsev D. V., Sokolov A. Е., Zukov R. A., Berezovski M. V., Tomilin F. N., Fedorov D. G., Alexeev Y., Kichkailo A. S.
Заглавие : The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer
Место публикации : Mol. Ther. Nucl. Acids. - 2021. - Vol. 25. - P.316-327. - ISSN 21622531 (ISSN), DOI 10.1016/j.omtn.2021.07.015
Примечания : Cited References: 84. - The research was performed using equipment of the Shared Core Facilities of Molecular and Cell Technologies at Krasnoyarsk State Medical University. The synchrotron SAXS data were collected at beamline P12 operated by EMBL Hamburg at the PETRA III storage ring (DESY, Hamburg, Germany). A.S.K. is grateful to Aptamerlab LLC for the assistance in aptamer design and 3D structure analyses. We thank Ivan Lapin for his help with microscopic analyses. Microscopic analyses using Carl Zeiss LSM 800 were carried out at the Center for Bioassay, Nanotechnology and Nanomaterials Safety (“Biotest-Nano”) (Multiple-Access Center, Tomsk State University, Tomsk, Russia). D.M. also thanks the CSC-IT Center in Espoo, Finland, for providing computational resources. The study was supported by a grant from the Russian Science Foundation (project number 21-73-20240) for A.S.K. R.V.M aknowledges Russian Foundation for Basic Research (project number 19-32-90266) for funding. D.G.F. acknowledges financial support by JSPS KAKENHI, grant number 19H02682. D.S.M. acknowledges financial support by BMBF grant number 16QK10A (SAS-BSOFT). Y.A.’s work at Argonne National Laboratory was supported by the US Department of Energy, Office of Science, under contract DE-AC02-06CH11357. D.M. received funding as a part of BioExcel CoE (https://bioexcel.eu/), a project funded by the European Union contracts H2020-INFRAEDI-02-2018-823830 and H2020-EINFRA-2015-1-675728. V.M. thanks Russian Foundation for Basic Research (project number 19-03-00043) for funding
Аннотация: Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.
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20.

Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Moryachkov R. V., Morozov D., Mironov V., Shchugoreva I., Artyushenko P. V., Zamay G. S., Molodenskiy D. S., Zabluda V. N., Kichkailo A.S., Sokolov A. Е.
Заглавие : The role of small-angle X-ray scattering and molecular simulations in 3D structure elucidation of a DNA aptamer-cancer cells magnetic separation agent
Коллективы : International Baltic Conference on Magnetism: focus on nanobiomedicine and smart materials, Балтийский федеральный университет им. И. Канта
Место публикации : 4th International Baltic Conference on Magnetism (IBCM 2021): Book of abstracts. - 2021. - P.168
Примечания : Cited References: 2. - The reported study was funded by RFBR, project number 19-32-90266
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