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1.
Gorban, A.
Codon usage trajectories and 7-cluster structure of 143 complete bacterial genornic sequences / A. . Gorban, T. . Popova, A. . Zinovyev> // Physica A. - 2005. -
Vol. 353
. - P. 365-387,
DOI
10.1016/j.physa.2005.01.043. - Cited References: 46 . - ISSN 0378-4371
РУБ
Physics, Multidisciplinary
Рубрики:
DNA
-BASE COMPOSITION
ASYMMETRIC SUBSTITUTION PATTERNS
PROTEIN-CODING REGIONS
MICROBIAL GENOMES
GENE IDENTIFICATION
MARKOV-MODELS
G+C CONTENT
BIAS
PREDICTION
SELECTION
Кл.слова (ненормированные):
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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Держатели документа:
Univ Leicester, Dept Math, Leicester LE1 7RH, Leics, England
RAS, SB, Inst Computat Modelling, Krasnoyarsk, Russia
Bures Sur Yvette & Bioinformat Serv Inst Curie, Inst Hautes Etudes Sci, Paris, France
ИВМ СО РАН
Department of Mathematics, University of Leicester, Leicester, University Road, Leicester LE1 7RH, United Kingdom
Institute of Computational Modelling, SB RAS, Krasnoyarsk, Russian Federation
Institut des Hautes Etudes Scientifiques, Bures-sur-Yvette and Bioinformatics Service of Institut Curie, Paris, France
Доп.точки доступа:
Popova, T.; Zinovyev, A.
}
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2.
Selection of
DNA
aptamers for breast cancer / G. S. Zamay, I. V. Belyanina, A. S. Zamay [et al.]> // Biochem. Mosc.-Suppl. Ser. B-Biomed. Chem. - 2016. -
Vol. 10
,
Is. 2
. - P. 158-164,
DOI
10.1134/S1990750816020128. - Cited References:23 . - ISSN 1990-7508. - ISSN 1990-7516
РУБ
Biochemistry & Molecular Biology
Рубрики:
BIOMARKERS
MORTALITY
PATTERNS
Кл.слова (ненормированные):
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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Публикация на русском языке
Селекция ДНК-аптамеров для диагностики рака молочной железы [Текст] / Г. С. Замай [и др.] // Биомедицинская химия. - Москва : Научно-исследовательский институт биомедицинской химии им. В.Н. Ореховича, 2016. - Т. 62 № 4. - С. 411-417
Держатели документа:
Kirensky Inst Phys, Krasnoyarsk, Russia.
Voino Yasenetski Krasnoyarsk State Med Univ, Ul Partizana Zheleznyaka 1, Krasnoyarsk 660022, Russia.
KKRCCC, Krasnoyarsk, Russia
Доп.точки доступа:
Zamay, G. S.; Замай, Г. С.; Belyanina, I. V.; Zamay, A. S.; Замай, Анна Сергеевна; Komarova, M. A.; Krat, A. V.; Eremina, E. N.; Zukov, R. A.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Zamay, T. N.; Замай, Т. Н.
}
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3.
Raman scattering in
dried
DNA
and crystalline amino acids / V. S. Gorelik [et al.]> // Phys. Wave Phenom. - 2016. -
Vol. 24
,
Is. 4
. - P. 272-278,
DOI
10.3103/S1541308X1604004X. - Cited References: 53. - The work was supported in part by the RFBR Projects 14-02-00190 and 16-52-00026 (BRFFR - RFBR F16R-063). . - ISSN 1541-308X
Перевод заглавия:
Комбинационное рассеяние света в высушенной ДНК и кристаллических аминокислот
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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Держатели документа:
Lebedev Physical Institute, Russian Academy of Sciences, Leninskiy pr. 53, Moscow, Russian Federation
Bauman Moscow State Technical University, ul. 2-ya Baumanskaya 5/1, Moscow, Russian Federation
Kirensky Institute of Physics, Siberian Branch of the Russian Academy of Sciences, Akademgorodok 50, str. 38, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Gorelik, V. S.; Zlobina, L. I.; Krylov, A. S.; Крылов, Александр Сергеевич; Sverbil, V. P.; Sverbil, P. P.
}
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4.
Magnetic and magnetooptical
properties of magnetic nanoparticles and
DNA
-Aptamers conjugates for medical application / A. E. Sokolov [et al.]> //
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. - The work was supported by the Ministry of Education and Science (Agreement No.14.607.21.0104 (RFMEFI60714X0104)) . - ISBN 978-5-904603-06-9
Кл.слова (ненормированные):
magnetic nanoparticles
--
magnetization
--
natural and magnetic circular dichroism
--
aptamers
--
bionanoconjugates
Доп.точки доступа:
Sokolov, A. E.; Соколов, Алексей Эдуардович; Ivanova, O. S.; Иванова, Оксана Станиславовна; Zabluda, V. N.; Заблуда, Владимир Николаевич; Dubynina, A. V.; Дубынина, А. В.; Semina, P. N.; Семина, Полина Николаевна; Zamay, G. S.; Замай, Г. С.; Zamay, T. N.; Замай, Татьяна Н.; Zamay, A. S.; Замай, Анна Сергеевна; Volochaev, M. N.; Волочаев, Михаил Николаевич; Svetlichnyi, V.; Светличный, Валерий; Lapin, I. N.; Лапин, И. Н.; Shabalina, A.; Шабалина, Анастасия; Euro-Asian Symposium "Trends in MAGnetism"(6 ; 2016 ; Aug. ; 15-19 ; Krasnoyarsk); "Trends in MAGnetism", Euro-Asian Symposium(6 ; 2016 ; Aug. ; 15-19 ; Krasnoyarsk); Институт физики им. Л.В. Киренского Сибирского отделения РАН
Нет сведений об экземплярах
}
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5.
The antitumor effect
of magnetic nanodisks and
DNA
aptamer conjugates / P. D. Kim [et al.]> // Dokl. Biochem. Biophys. - 2016. -
Vol. 466
,
Is. 1
. - P. 66-69,
DOI
10.1134/S1607672916010154. - Cited References:7. - This work was supported by the Russian Science Foundation (project no. 14-15-00805). . - ISSN 1607-6729. - ISSN 1608-3091
РУБ
Biochemistry & Molecular Biology + Biophysics
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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Публикация на русском языке
Противоопухолевый эффект конъюгатов магнитных нанодисков с ДНК-аптамерами [Текст] / П. Д. Ким [и др.] // Докл. Акад. наук : Наука, 2016. - Т. 466 № 5. - С. 616-619
Держатели документа:
Russian Acad Sci, Siberian Branch, Krasnoyarsk Res Ctr, Krasnoyarsk 660036, Russia.
Voinoyasenetskii State Med Univ, Minist Hlth Russian Federat, Ul Partizana Zheleznyaka 1, Krasnoyarsk 660022, Krasnoyarsk Kra, Russia.
Siberian Fed Univ, Svobodnyi Pr 79, Krasnoyarsk 660041, Russia.
Russian Acad Sci, Siberian Branch, Inst Chem & Chem Technol, Krasnoyarsk, Russia.
Russian Acad Sci, Siberian Branch, Inst Semicond Phys, Pr Akad Lavrenteva 13, Novosibirsk 630090, Russia.
Russian Acad Sci, Siberian Branch, Kirenskii Inst Phys, Krasnoyarsk 660036, Russia.
Astafev Krasnoyarsk State Pedag Univ, Ul A Lebedevoi 89, Krasnoyarsk 660049, Russia.
Доп.точки доступа:
Kim, P. D.; Ким, Пётр Дементьевич; Zamay, S. S.; Замай С. С.; 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.; Руденко, Роман Юрьевич; Dubinina, A. V.; Komarov, A. V.; Denisenko, V. V.; Komarova, M. A.; Sokolov, A. E.; Соколов, Алексей Эдуардович; Narodov, A. A.; Zjivaev, V. P.; Zamay, A. S.; Russian Science Foundation [14-15-00805]
}
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6.
Molecular design of
aptamer structure by computer simulations / I. Shchugoreva [et al.]> //
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. - 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 . - ISBN 978-5-904603-06-9
Кл.слова (ненормированные):
DNA
--
SELEX
--
SAXS
--
QM/MM
--
aptamer
--
G-quartets
Доп.точки доступа:
Shchugoreva, I.; Moryachkov, R.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Sokolov, A. E.; Соколов, Алексей Эдуардович; Spiridonova, V. A.; Спиридонова В. А.; Gruzinov, A.; Zamay, A. S.; Замай, Анна Сергеевна; Veprincev, D.; Zamay, G. S.; Замай Г. С.; Tomilin, F. N.; Томилин, Феликс Николаевич; Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич; Euro-Asian Symposium "Trends in MAGnetism"(6 ; 2016 ; Aug. ; 15-19 ; Krasnoyarsk); "Trends in MAGnetism", Euro-Asian Symposium(6 ; 2016 ; Aug. ; 15-19 ; Krasnoyarsk); Институт физики им. Л.В. Киренского Сибирского отделения РАН
Нет сведений об экземплярах
}
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7.
Magnetic nanoparticles and
DNA
-aptamers conjugates for cancer therapy / A. Е. Sokolov [et al.]> //
Int. Baltic Conf. Magnet. (IBCM-2017) : Focus on funcshionalized magnetic struct. for energy and biotech. : book of abstracts. - 2017. - P. 77. - Библиогр.: 4
Материалы конференции
Доп.точки доступа:
Sokolov, A. Е.; Соколов, Алексей Эдуардович; Ivanova, O. S.; Иванова, Оксана Станиславовна; Zabluda, V. N.; Заблуда, Владимир Николаевич; Dubinina, A. V.; Semina, P. N.; Семина, Полина Николаевна; Zamay, G. S.; Замай Г. С.; Zamay, T. N.; Zamay, S. S.; Замай С. С.; Volochaev, M. N.; Волочаев, Михаил Николаевич; Svetlichnyi, V.; Светличный В.; Lapin, I. N.; Лапин Иван; Shabalina, A.; Шабалина Анастасия; Solodova, O. V.; Солодова О. В.; International Baltic Conference on Magnetism: Focus on funcshionalized magnetic structures for energy and biotechnology (2 ; 2017 ; 20-24 Aug. ; Svetlogorsk); Балтийский федеральный университет им. И. Канта
}
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8.
In vivo cancer
cells elimination guided by aptamer-functionalized gold-coated magnetic nanoparticles and controlled with low frequency alternating magnetic field / I. V. Belyanina [et al.]> // Theranostics. - 2017. -
Vol. 7
,
Is. 13
. - P. 3326-3337,
DOI
10.7150/thno.17089. - 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). . - ISSN 1838-7640
РУБ
Medicine, Research & Experimental
Рубрики:
PHOTOTHERMAL THERAPY
INTEGRIN ACTIVATION
FIBRONECTIN
STIMULATION
Кл.слова (ненормированные):
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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Держатели документа:
Krasnoyarsk State Med Univ, Krasnoyarsk, Russia.
Russian Acad Sci, KSC Siberian Branch, Fed Res Ctr, Krasnoyarsk, Russia.
Siberian Fed Univ, Krasnoyarsk, Russia.
Univ Ottawa, Dept Chem & Biomol Sci, Ottawa, ON, Canada.
Inst Computat Modeling RAS SB, Krasnoyarsk, Russia.
Доп.точки доступа:
Belyanina, I. V.; Zamay, T. N.; Замай Т. Н.; Zamay, G. S.; Замай, Галина Сергеевна; Zamay, S. S.; Замай С. С.; Kolovskaya, Olga S.; Ivanchenko, Tatiana I.; Denisenko, Valery V.; Kirichenko, Andrey K.; Glazyrin, Yury E.; Garanzha, Irina V.; Grigorieva, Valentina V.; Shabanov, A. V.; Шабанов, Александр Васильевич; Veprintsev, Dmitry V.; Sokolov, A. E.; Соколов, Алексей Эдуардович; Sadovskii, Vladimir M.; Gargaun, Ana; Berezovski, M. V.; Kichkailo, Anna S.; Russian Scientific Fund [14-15-00805]
}
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9.
Magnetic nanoparticles and
DNA
-aptamers conjugates for diagnostics and therapy of cancer : Invited / A. E. Sokolov [et al.]> //
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
Материалы совещания
Доп.точки доступа:
Ovchinnikov, S. G. \предс. прогр. ком.\; Овчинников, Сергей Геннадьевич; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Zamay, S. S.; Замай С. С.; Zamay, T. ; Замай Татьяна; Svetlichnyi, V.; Светличный В.; Velikanov, D. A.; Великанов, Дмитрий Анатольевич; 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)
Нет сведений об экземплярах (Источник в БД не найден)
}
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10.
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. ; предс. прогр. ком. S. G. Ovchinnikov. - Krasnoyarsk : [s. n.], 2017. - 30 p.
Содержание:
Bondarev, I. A. Magnetic and transport properties of the epitaxial Fe3Si film on a Si substrate
/ I. A. Bondarev. -
P
.25
Yakovlev, I. A. The magnetic anisotropy of the Fe and Fe(1-x)Si(x) thin films depend on
/ I. A. Yakovlev [и др.]. -
P
.12
Другие авторы: Belyaev B. A., Rautskii M. V., Tarasov, I. A., Varnakov S. N, Ovchinnikov, S. G.
Popkov, S. I. Inverted opals as the Josephson networks of weak links
: Invited / S. I. Popkov [и др.]. -
P
.24
Другие авторы: Gokhfeld D. M., Bykov A., Mistonov A., Shabanov A., Terentiev K.
Nikolaev, S. Electronic structure and Fermi surface within the cluster perturbation theory in X-operators representation
: Invited / S. Nikolaev, V. I. Kuz'min, S. G. Ovchinnikov. -
P
.27
Fedorov, A. S. DFT investigation of electronic and optical magnetic properties of one dimensional transition metal halide structuresTmHaI3
: Invited / A. S. Fedorov [и др.]. -
P
.20
Другие авторы: Kuzubov A. A., Kovaleva E. A., Popova M. I., Kholtobina A. S., Mikhaleva N. S., Visotin M. A.
Ovchinnikov, S. G. 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
: Invited / S. G. Ovchinnikov [и др.]. -
P
.26
Другие авторы: Orlov Yu. S., Nikolaev S., Nesterov A., Ovchinnikova T.
Tarasov, I. A. Extremely high magnetic-field sensitivity of charge transport in the Mn/SiO2/p-Si hybrid structure
/ I. A. Tarasov [и др.]. -
P
.21
Другие авторы: Smolyakov D. A., Rautskii M. V., Lukyanenko A. V., Yakovlev I. A., Ovchinnikov S. G., Volkov N. V.
Volkov, N. V. Marnetic-field sensitivity of charge transport in silicon-based hybrid structures
: Invited / N. V. Volkov [et al.]. -
P
.10
Другие авторы: Tarasov A. S., Rautskii M. V., Lukyanenko A. V., Varnakov S. N., Bondarev I. A., Ovchinnikov S. G.
Lukyanenko, A. V. 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.]. -
P
.28
Другие авторы: Tarasov A. S., Tarasov I. A., Bondarev I. A., Smolyarova T. E., Yakovlev I. A., Volochaev M. N., Varnakov S. N., Ovchinnikov S. G., Volkov N. V.
Rautskii, M. V. Magnetic field-driven lateral photovoltaic effect in the Fe/SiO2/p-Si hibrid structure with the Scottky barrier
/ M. V. Rautskii [и др.]. -
P
.29
Другие авторы: Tarasov A. S., Varnakov S. N., Bondarev I. A., Volochaev M. N., Lukyanenko A. V., Volkov N. V.
Moryachkov, R. Small angle X-ray scattering and atomic structure of aptamer biomolecules
/ R. Moryachkov [и др.]. -
P
.14-15
Другие авторы: Tomilin F. N., Shchugoreva I., Spiridonova V., Peters G., Zabluda V.
Tarasov, I. A. Iron silicides and pure iron epitaxial and highly-textured nanostructures on silicon: growth and their physical properties
: Invited / I. A. Tarasov [и др.]. -
P
.23
Другие авторы: Visotin M. A., Solovyov L. A., Rautskii M. V., Zhandun, V. S., Nemtsev I. V., Yakovlev I. A., Varnakov S. N, Ovchinnikov, S. G.
Sokolov, A. E. Magnetic nanoparticles and
DNA
-aptamers conjugates for diagnostics and therapy of cancer
: Invited / A. E. Sokolov [и др.]. -
P
.13
Другие авторы: Zamay S., Zamay T., Svetlichnyi V., Velikanov D.
Sandalov, I. S. The microscopic origin of ferromagnetism in Fe silicides
: Invited / I. S. Sandalov [и др.]. -
P
.16
Другие авторы: Zamkova N. G., Zhandun V. S., Ovchinnikov, S. G.
Материалы конференции
Держатели документа:
Институт физики им. Л.В. Киренского СО РАН
Доп.точки доступа:
Ovchinnikov, S. G. \предс. прогр. ком.\; Овчинников, Сергей Геннадьевич; Lukyanenko, A. V.; Varnakov, S. N.; Bondarev, I. A.; Ovchinnikov, S. G.; Tarasov, I. A.; Svetlichnyi, V.; Velikanov, D. A.; Spiridonova, V.; Peters, G.; Zabluda, V. N.; Popova, M. I.; Kholtobina, A. S.; Mikhaleva, N. S.; Visotin, M. A.; Yakovlev, I. A.; Volkov, N. V.; Rautskii, M. V.; Zhandun, V. S.; Nemtsev, I. V.; Varnakov, S. N; Mistonov, A.; Shabanov, A. V.; Terentiev, K. Yu.; Nesterov, A.; Ovchinnikova, T.; Smolyarova, T. E.; Volochaev, M. N.; 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)
Свободных экз. нет
}
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11.
Magnetic nanoconstructions of
iron oxides coated with arabinogalactan functionalized with
DNA
aptamer / S. V. Stolyar [et al.]> // J. Phys. Conf. Ser. - 2019. -
Vol. 1399
. - Ст. 022026,
DOI
10.1088/1742-6596/1399/2/022026. - Cited References: 6 . - ISSN 1742-6588. - ISSN 1742-6596
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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Держатели документа:
Siberian Federal University, Krasnoyarsk, Russia
Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia
Krasnoyarsk Scientific Center, Federal Research Center KSC SB RAS Krasnoyarsk, Russia
Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Krasnoyarsk, 660022, Russia
Astrakhan State University, Tatisheva 20 A, Astrakhan, 414056, Russia
College of Biotechnology, Al-Qasim Green University, Iraq
Доп.точки доступа:
Stolyar, S. V.; Столяр, Сергей Викторович; Chekanova, L. A.; Чеканова, Лидия Александровна; Yaroslavtsev, R. N.; Ярославцев, Роман Николаевич; Komogortsev, S. V.; Комогорцев, Сергей Викторович; Gerasimova, Yu. V.; Герасимова, Юлия Валентиновна; Bayukov, O. A.; Баюков, Олег Артемьевич; Volochaev, M. N.; Волочаев, Михаил Николаевич; Iskhakov, R. S.; Исхаков, Рауф Садыкович; Garanzha, I. V.; Kolovskaya, O. S.; Bairmani, M. Sh.; Zamay, T. N.; International Scientific Conference "Conference on Applied Physics, Information Technologies and Engineering"(25-27 September 2019 ; Krasnoyarsk, Russian Federation)
}
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12.
Conformational changes in
DNA
aptamers upon binding to Pb ions / R. V. Moryachkov, A. N. Berlina, P. V. Artyushenko [et al.]> //
The Fifth Asian School-Conference on Physics and Technology of Nanostructured Materials : Proceedings. - VLadivostok : Dalnauka Publishing, 2020. - Ст. VII.31.01p. - P. 193. - The reported study was funded by RFBR, project number 19-32-90266. . - ISBN 978-5-8044-1698-1
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Доп.точки доступа:
Moryachkov, R. V.; Морячков, Роман Владимирович; Berlina, A. N.; Artyushenko, P. V.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Peters, G. S.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Asian School-Conference on Physics and Technology of Nanostructured Materials(5 ; 2020 ; 30 Jul - 3 Aug ; Vladivostok); Азиатская школа-конференция по физике и технологии наноструктурированных материалов(5 ; 2013 ; 30 июля - 3 авг. ; Владивосток)
}
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13.
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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14.
Obtaining and properties
of biomagnetic nanoconjugates based on
DNA
aptamers and magnetic nanoparticles for magnetodynamic cell therapy / A. Е. Sokolov, A. V. Kurilova, V. A. Svetlichniy [et al.]> //
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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Доп.точки доступа:
Sokolov, A. Е.; Соколов, Алексей Эдуардович; Kurilova, A. V.; Svetlichniy, V. A.; Velikanov, D. A.; Великанов, Дмитрий Анатольевич; Sherepa, A. V.; Volochaev, M. N.; Волочаев, Михаил Николаевич; Goncharova, D. A.; Shabalina, A. V.; Asian School-Conference on Physics and Technology of Nanostructured Materials(5 ; 2020 ; 30 Jul - 3 Aug ; Vladivostok); Азиатская школа-конференция по физике и технологии наноструктурированных материалов(5 ; 2013 ; 30 июля - 3 авг. ; Владивосток)
}
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15.
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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Держатели документа:
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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16.
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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17.
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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18.
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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19.
Investigation of the
spatial structure of bionanoconjugates based on
DNA
aptamers by synchrotron methods / R. V. Moryachkov, V. N. Zabluda, I. A. Shchugoreva [et al.]> //
International conference "Functional materials" : book of abstracts / ed. V. N. Berzhansky ; org. com. S. G. Ovchinnikov [et al.]. - Simferopol, 2021. - P. 310. - Библиогр.: 3 назв. - The research was carried out with a grant from the Russian Science Foundation № 21-12-00226, https://rscf.ru/project/21-12-00226/
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Доп.точки доступа:
Berzhansky, V. N. \ed.\; Бержанский, Владимир Наумович; Ovchinnikov, S. G. \org. com.\; Овчинников, Сергей Геннадьевич; Moryachkov, R. V.; Морячков, Роман Владимирович; Zabluda, V. N.; Заблуда, Владимир Николаевич; Shchugoreva, Irina A.; Artyushenko, P. V.; Kichkaylo, A.S.; Spiridonova, V. A.; Berlina, A. N.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; "Functional materials", International conference(2021 ; Oct. 4-8 ; Alushta, Russia); Крымский федеральный университет имени В.И. Вернадского
}
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20.
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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