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1Academic Journal
Source: Школа-конференция молодых ученых, аспирантов и студентов «Генетические технологии в микробиологии и микробное разнообразие».
Subject Terms: направленный мутагенез, гомологичная рекомбинация, Pseudomonas, РНК-полимераза, салицилат, регуляция экспрессии генов, промотор
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2Academic Journal
Authors: V.M. Nikolaev, N.K. Chirikova, S.I. Sofronova, E.K. Rumyancev, A.G. Vasileva, A.N. Romanova
Source: Yakut Medical Journal. :95-101
Subject Terms: геликаза, терпеноиды, 30-подобная протеаза, папаиноподобная протеаза, SARS-CoV-2, papain-like protease, лектины, phenolic compounds, alkaloids, virus taxonomy, RNA-dependent RNA polymerase, lectins, 3. Good health, helicase, ангиотензинпревращающий фермент 2, жизненный цикл вируса, таксономия вируса, terpenoids, angiotensin-converting enzyme 2, virus life cycle, алкалоиды, РНК-зависимая РНК-полимераза, 3C-like protease, фенольные соединения
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3Academic Journal
Authors: Ali A. Dawood, Али А. Давуд
Source: Medical Immunology (Russia); Том 24, № 3 (2022); 617-628 ; Медицинская иммунология; Том 24, № 3 (2022); 617-628 ; 2313-741X ; 1563-0625
Subject Terms: мутации, remdesivir, RdRp, S protein, mutation, ремдесивир, РНК-зависимая РНК-полимераза, спайковый белок
File Description: application/pdf
Relation: https://www.mimmun.ru/mimmun/article/view/2486/1559; Baum A., Fulton B.O., Wloga E., Copin R., Pascal K.E., Russo V., Giordano S., Lanza K., Negron N., Ni M., Wei Y., Atwal G.S., Murphy A.J., Stahl N., Yancopoulos G.D., Kyratsous C.A. Antibody cocktail to SARSCoV-2 spike protein prevents rapid mutational escape seen with individual antibodies. Science, 2020, Vol. 369, pp. 1014-1018.; Choy K.-T., Wong A.Y.-L., Kaewpreedee P., Sia S.F., Chen D., Hui K.P.Y., Chu D.K.W., Chan M.C.W., Cheung P.P.-H., Huang X., Peiris M., Yen H.-L. Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARSCoV-2 replication in vitro. Antiviral Res., 2020, Vol. 178, 104786. doi:10.1016/j.antiviral.2020.104786.; Dawood A., Altobje M., Alnori H. Compatibility of the ligand binding sites in the spike glycoprotein of covid-19 with those in the aminopeptidase and the caveolins 1, 2 proteins. Res. J. Pharm. Tech., 2021, Vol. 14, no. 9, pp. 4760-4766.; Dawood A., Altobje M., Alrassam Z. Molecular docking of SARS-CoV-2 nucleocapsid protein with angiotensin-converting enzyme II. Mikrobiol. Zhu, 2021, Vol. 83, no. 2, pp. 82-92.; Dawood A., Altobje M. Inhibition of N-linked glycosylation by nunicamycin may contribute to the treatment of SARS-CoV-2. Microbiol. Path., 2020, Vol. 149, 104586. doi:10.1016/j.micpath.2020.104586.; Dawood A. Glycosylation, ligand binding sites and antigenic variations between membrane glycoprotein of COVID-19 and related coronaviruses. Vacunas. 2021, Vol. 22, no. 1, pp. 1-9.; Dawood A. Identification of CTL and B-cell epitopes in the Nucleocapsid Phosphoprotein of COVID-19 using Immunoinformatics. Microbiol. J., 2021, Vol. 83, no. 1, pp. 78-86.; Dawood A. New variant of SARS-CoV-2 in South Africa. Prog. Med. Sc., 2021, Vol. 5, no. 1, pp. 1-2.; Dawood A. Using remdesivir and dexamethasone for treatment of SARS-CoV-2 shortens the patient’s stay in the hospital. Asi an J. Pharm. Res., 2021, Vol. 11, Iss. 2, 138-0. doi:10.52711/2231-5691.2021.00026.; Deshpande R., Tiwari P., Nyayanit N., Modak M. In silico molecular docking analysis for repurposing therapeutics against multiple proteins from SARS-CoV-2. Eur. J. Pharmacol., 2020, Vol. 886, 173430. doi.org/10.1016/j.ejphar.2020.173430.; Eskier D., Karakülah G., Suner A., Oktay Y. RdRp mutations are associated with SARS-CoV-2 genome evolution. Peer J., 2020, Vol. 8, e9587. doi:/10.7717/peerj.9587.; Eweas A., Alhossary A., Abdul-Moneim A. Molecular Docking Reveals ivermectin and remdesivir as potential repurposed drugs against SARS-CoV-2. Front. Microbiol., 2021, Vol. 11, e592908. doi:10.3389/fmicb.2020.592908.; Garvin M.R., Prates E.T., Pavicic M., Jones P., Amos B.K., Geiger A., Shah M.B., Streich J., Gazolla J.G.F.M., Kainer D., Cliff A., Romero J., Keith N., Brown J.B., Jacobson D. Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Genome Biol., 2020, Vol. 21, 304. doi:10.1186/s13059-020-02191-0.; Grein J., Ohmagari N., Shin D., Diaz G., Asperges E. Compassionate use of remdesivir for patients with severe Covid-19. N. Engl. J. Med., 2020, Vol. 382, pp. 2327-2336.; Hall Jr., Ji H-F. A search for medications to treat COVID-19 via in silico molecular docking models of the SARS-CoV-2 spike glycoprotein and 3CL protease. Travel Med. Infect. Dis., 2020, Vol. 35, 101646. doi: 0.1016/j.tmaid.2020.101646.; Henderson R., Edwards R.J., Mansouri K., Janowska K., Stalls V., Gobeil S.M.C., Kopp M., Li D., Parks R., Hsu A.L., Borgnia M.J., Haynes B.F., Priyamvada acharya controlling the SARS-CoV-2 spike glycoprotein conformation. Nat. Struct. Mol. Biol., 2020, Vol. 27, pp. 925-933.; Ilmjärv S., Abdul F., Acosta-Gutiérrez S., Estarellas C., Galdadas I., Casimir M., Alessandrini M., Gervasio F.L., Krause K.-H. Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Sci. Rep., 2021, Vol. 11, 13705. doi:10.1038/s41598021-91662-w.; Jean S., Lee I., Hsueh R. Treatment options for COVID-19: the reality and challenges. J. Microbiol. Immunol. Infect., 2020, Vol. 53, pp. 436-443.; Kumar Y., Singh H., Patel C.N. In silico prediction of potential inhibitors for the main protease of SARSCoV-2 using molecular docking and dynamics simulation based drug-repurposing. J. Infect. Public Health, 2020, Vol. 13, pp. 1210-1223.; Mari A., Roloff T., Stange M., Søgaard K.K., Asllanaj E., Tauriello G., Alexander L.T., Schweitzer M., Leuzinger K., Gensch A., Martinez A.E., Bielicki J., Pargger H., Siegemund M., Nickel C.H., Bingisser R., Osthoff M., Bassetti S., Sendi P., Battegay M., Marzolini C., Seth-Smith H.M.B., Schwede T., Hirsch H.H., Egli A. Global genomic analysis of SARS-CoV-2 RNA dependent RNA polymerase evolution and antiviral drug resistance. Microorganisms, 2021, Vol. 9, no. 5, 1094. doi:10.3390/microorganisms9051094.; Nguyen H., Thai N., Truong D., Li M. Remdesivir Strongly Binds to Both RNA-Dependent RNA polymerase and Main Protease of SARS-CoV-2: Evidence from Molecular Simulations. J. Phys. Chem., 2020, Vol. 124, pp. 11337-11348.; Pachetti M., Marini B., Benedetti F., Giudici F., Mauro E., Storici P., Masciovecchio C., Angeletti S., Ciccozzi M., Gallo R.C., Zella D., Ippodrino R. Emerging SARS-CoV-2 mutation hot spots include a novel RNAdependent-RNA polymerase variant. J. Transl. Med., 2020, Vol. 18, no. 1, 179. doi.org/10.1186/s12967-020-02344-6.; Sada M., Saraya T., Ishii H., Okayama K., Hayashi Y., Tsugawa T., Nishina A., Murakami K., Kuroda M., Ryo A., Kimura H. Detailed molecular interactions of favipiravir with SARS-CoV-2, SARS-CoV, MERS-CoV, and influenza virus polymerases in silico. Microorganisms, 2020, Vol. 8, no. 10, 1610. doi:10.3390/microorganisms8101610.; Salleh M.Z., Derrick J.P., Deris Z.Z. Structural evaluation of the spike glycoprotein variants on SARS-CoV-2 transmission and immune evasion. Inter. J. Mol. Sci., 2021, Vol. 22, no. 14, 7425. doi.org/10.3390/ijms22147425.; Senger M.R., Evangelista T.C.S., Dantas R.F., Santana M.V.D.S., Gonçalves L.C.S., de Souza Neto L.R., Ferreira S.B., Silva-Junior F.P. COVID-19: molecular targets, drug repurposing and new avenues for drug discovery. Mem. Inst. Oswaldo Cruz, 2020, Vol. 115, e200254. doi:10.1590/0074-02760200254.; Shaeen A., Sattar N., Ibrahim M., Irfan M. Role of Remdesivir in COVID-19. Aus. J. Pulm. Res. Med., 2021, Vol. 8, no. 1, 1071.; Sheahan T.P., Sims A.C., Leist S.R., Schafer A., Won J. Comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against MERS-CoV. Nat. Commun., 2020, Vol. 11, no. 1, 222. doi:10.1038/s41467-019-13940-6.; Shehroz M., Zaheer T., Hussain T. Computer-aided drug design against spike glycoprotein of SARS-CoV-2 to aid COVID-19 treatment. Heliyon, 2020, Vol. 6, no. 10, e05278. doi.org/10.1016/j.heliyon.2020.e05278.; Showers W., Leach S., Kechris K., Strong M. Analysis of SARS-CoV-2 Mutations over time reveals increasing prevalence of variants in the spike protein and RNA-dependent RNA polymerase. bioRxiv, 2021. doi:10.1101/2021.03.05.433666.; Sun C., Zhang J., Wei J., Zheng X., Zhao X., Fang Z., Xu D., Yuan H., Liu Y. Screening, simulation, and optimization design of small molecule inhibitors of the SARS-CoV-2 spike glycoprotein. PLoS One, 2021, Vol. 16, no. 1, e0245975. doi:10.1371/journal.pone.0245975.; Walls C., Park Y.-J., Tortorici A., Wall A., Mcguire T., Veesler D. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell, 2020, Vol. 181, pp. 281.e6-292.e6.; Wang M., Cao R., Zhang L., Yang X., Liu J., Xu M., Shi Z., Hu Z., Zhong W., Xiao G. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res., 2020, Vol. 30, pp. 269-271.; Williamson B.N., Feldmann F., Schwarz B., Meade-White K., Porter D.P., Schulz J., van Doremalen N., Leighton I., Yinda C.K., Pérez-Pérez L., Okumura A., Lovaglio J., Hanley P.W., Saturday G., Bosio C.M., Anzick S., Barbian K., Cihlar T., Martens C., Scott D.P., Munster V.J., de Wit E. Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-19. Nature, 2020, Vol. 585, pp. 273-276.; Wu A., Peng Y., Huang B., Ding X., Wang X., Niu P., Meng J., Zhu Z., Zhang Z., Wang J., Sheng J., Quan L., Xia Z., Tan W., Cheng G., Jiang T. Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. Cell Host Microbe, 2020, Vol. 27, pp. 325-328.; Wu C., Chen X., Cai Y., Xia J., Zhou X. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China. JAMA Intern. Med., 2020, Vol. 180, no. 7, pp. 1-11.; Yin W., Mao C., Luan X., Shen D.-D., Shen Q., Su H., Wang X., Zhou F., Zhao W., Gao M., Chang S., Xie Y.C., Tian G., Jiang H.-W., Tao S.-C., Shen J., Jiang Y., Jiang H., Xu Y., Zhang S., Zhang Y., Xu H.E. Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir. Science, 2020, Vol. 368, pp. 1499-1504.; Yurkovetskiy L. Wang X., Pascal K.E., Tomkins-Tinch C., Nyalile T.P., Wang Y., Baum A., Diehl W.E., Dauphin A., Carbone C., Veinotte K., Egri S.B., Schaffner S.F., Lemieux J.E., Munro J.B., Rafique A., Barve A., Sabeti P.C., Kyratsous C.A., Dudkina N.V., Shen K., Luban J. Structural and functional analysis of the D614G SARSCoV-2 spike protein variant. Cell, 2020, Vol. 183, pp. 739-751.e8.; Zhang Q., Xiang R., Huo S., Zhou Y., Jiang S., Wang Q., Yu F. Molecular mechanism of interaction between SARS-CoV-2 and host cells and interventional therapy. Sig. Transduct. Target. Ther., 2021, Vol. 6, no. 1, 233. doi:10.1038/s41392-021-00653-w.; Zhu N., Zhang D., Wang W., Li X., Yang B., Song J., Zhao X., Huang B., Shi W., Lu R., Niu P., Zhan F., Ma X., Wang D., Xu W., Wu G., Gao G.F., Tan W. A novel coronavirus from patients with pneumonia in China, 2019. N. Engl. J. Med., 2020, Vol. 382, pp. 727-733.; https://www.mimmun.ru/mimmun/article/view/2486
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4Academic Journal
Source: Doklady of the National Academy of Sciences of Belarus; Том 62, № 5 (2018); 601-607 ; Доклады Национальной академии наук Беларуси; Том 62, № 5 (2018); 601-607 ; 2524-2431 ; 1561-8323 ; 10.29235/1561-8323-2018-62-5
Subject Terms: Escherichia coli, T7 bacteriophage RNA polymerase, DNA-affinity domain of Sulfolobus solfataricus, РНК-полимераза бактериофага T7, ДНК-аффинный домен Sulfolobus solfataricus
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Relation: https://doklady.belnauka.by/jour/article/view/558/562; Bundy, B. C. Escherichia coli-based cell-free synthesis of virus-like particles / B. C. Bundy, M. J. Franciszkowicz, J. R. Swartz // Biotechnol. Bioeng. - 2008. - Vol. 100, N 1. - P. 28-37. https://doi.org/10.1002/bit.21716; Bundy, B. C. Efficient disulfide bond formation in virus-like particles / B. C. Bundy, J. R. Swartz // J. Biotechnol. -2011. - Vol. 154, N 4. - P. 230-239. https://doi.org/10.1016/jjbiotec.2011.04.011; The incorporation of the A2 protein to produce novel QP virus-like particles using cell-free protein synthesis / M. T. Smith [et al.] // Biotechnol. Prog. - 2012. - Vol. 28, N 2. - P. 549-555. https://doi.org/10.1002/btpr.744; Cell-free synthesis of functional aquaporin Z in synthetic liposomes / N. T. Hovijitra [et al.] // Biotechnol. Bioeng. -2009. - Vol. 104, N 1. - P. 40-49. https://doi.org/10.1002/bit.22385; On-chip automation of cell-free protein synthesis: new opportunities due to a novel reaction mode / V. Georgi [et al.] // Lab. Chip. - 2016. - Vol. 16, N 2. - P. 269-281. https://doi.org/10.1039/c5lc00700c; Caschera, F. Preparation of amino acid mixtures for cell-free expression systems / F. Caschera, V. Noireaux // Biotechniq. - 2015. - Vol. 58. - P. 40-43. https://doi.org/10.2144/000114249; Roberts, J. W. Termination factor for RNA synthesis / J. W. Roberts // Nature. - 1969. - Vol. 224, N 5225. - P. 11681174. https://doi.org/10.1038/2241168a0; Studier, F. W. T7 expression systems for inducible production of proteins from cloned genes in E. coli / F. W. Studier // Curr. Protoc. Mol. Biol. - 2018. - Vol. 124, N 1. - e63. https://doi.org/10.1002/cpmb.63; Создание рекомбинантного штамма Escherichia coli - продуцента РНК-полимеразы бактериофага Т7 / И. С. Казловский [и др.] // Микробные биотехнологии: фундаментальные и прикладные аспекты. - Минск: Беларуская навука, 2016. - Т. 8. - С. 72-81.; A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro / Y. Wang [et al.] // Nucleic Acids Res. - 2004. - Vol. 32, N 3. - P. 1197-1207. https://doi.org/10.1093/nar/gkh271; Production of thermostable DNA polymerase suitable for whole-blood polymerase chain reaction / A. S. Korovashkina [et al.] // Biochemistry and Biotechnology: Research and Development / eds. S. D. Varfolomeev, G. E. Zaikov, L. P. Krylova. -New York: Nova Science Publishers, Inc., 2012. - Р. 1-5.; Quan, J. Circular polymerase extension cloning of complex gene libraries and pathways / J. Quan, J. Tian // PLoS ONE. - 2009. - Vol. 4, N 7. - e6441. https://doi.org/10.1371/journal.pone.0006441; You, C. Simple cloning via direct transformation of PCR product (DNA multimer) to Escherichia coli and Bacillus subtilis / C. You, X. Z. Zhang, Y. H. P. Zhang // Appl. Environ. Microbiol. - 2012. - Vol. 78, N 5. - P. 1593-1595. https://doi. org/10.1128/aem.07105-11; Construction and expression of a modular gene encoding bacteriophage T7 RNA polymerase / N. Arnaud [et al.] // Gene. -1997. - Vol. 199, N 1-2. - P. 149-156. https://doi.org/10.1016/s0378-1119(97)00362-4; https://doklady.belnauka.by/jour/article/view/558
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5Academic Journal
Authors: N. S. Gerasimova, N. A. Pestov, O. I. Kulaeva, D. V. Nikitin, M. P. Kirpichnikov, V. M. Studitsky, Надежда Сергеевна Герасимова, Николай Александрович Пестов, Ольга Игоревна Кулаева, Дмитрий Валерьевич Никитин, Михаил Петрович Кирпичников, Василий Михайлович Студитский
Contributors: Российский научный фонд
Source: Vestnik Moskovskogo universiteta. Seriya 16. Biologiya; № 3 (2015); 21-25 ; Вестник Московского университета. Серия 16. Биология; № 3 (2015); 21-25 ; 0137-0952
Subject Terms: обзор, repair, nucleosome, histone, DNA, DNA breaks, oxidative stress, RNA polymerase II, review, репарация, нуклеосома, гистон, ДНК, разрывы ДНК, окислительный стресс, РНК-полимераза II
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N 6. P. 1463—1471.; Hayes J.J., Tullius T.D., Wolffe A.P. The structure of DNA in a nucleosome // Proc. Natl. Acad. Sci. USA. 1990. Vol. 87. N 19. P. 7405—7409.; Strand J.M., Scheffler K., Bj ras M., Eide L. The distribution of DNA damage is defined by region-specific susceptibility to DNA damage formation rather than repair differences // DNA Repair (Amst.). 2014. Vol. 18. P. 44—51.; Tijsterman M., de Pril R., Tasseron-de Jong J.G., Brouwer J. RNA Polymerase II transcription suppresses nucleosomal modulation of UV-induced (6—4) photoproduct and cyclobutane pyrimidine dimer repair in yeast // Mol. Cell. Biol. 1999. Vol. 19. N 1. P. 934—940.; Odell I.D., Wallace S.S., Pederson D.S. Rules of engagement for base excision repair in chromatin // J. Cell. Physiol. 2013. Vol. 228. N 2. P. 258—266.; Nouspikel T., Hanawalt P.C. DNA repair in terminally differentiated cells // DNA repair (Amst.). 2002. Vol. 1. N 1. P. 59—75.; Blainey P.C., Luo G., Kou S.C., Mangel W.F., Verdine G.L., Bagchi B., Xie X.S. Nonspecifically bound proteins spin while diffusing along DNA // Nat. Struct. Mol. Biol. 2009. Vol. 16. N 12. P. 1224—1229.; Odell I.D., Newick K., Heintz N.H., Wallace S.S., Pederson D.S. Non-specific DNA binding interferes with the efficient excision of oxidative lesions from chromatin by the human DNA glycosylase, NEIL1 // DNA repair (Amst.). 2010. Vol. 9. N 2. P. 134—143.; Odell I.D., Barbour J.E., Murphy D.L., Della-Maria J.A., Sweasy J.B., Tomkinson A.E., Wallace S.S., Pederson D.S. Nucleosome disruption by DNA ligase III-XRCC1 promotes efficient base excision repair // Mol. Cell. Biol. 2011. Vol. 31. N 22. P. 4623—4632.; Hinz J.M., Rodriguez Y., Smerdon M.J. Rotational dynamics of DNA on the nucleosome surface markedly impact accessibility to a DNA repair enzyme // Proc. Natl. Acad. Sci. USA. 2010. Vol. 107. N 10. P. 4646—4651.; Murr R., Loizou J.I., Yang Y.G., Cuenin C., Li H., Wang Z.Q., Herceg Z. Histone acetylation by Trrap-Tip60 modulates loading of repair proteins and repair of DNA double-strand breaks // Nat. Cell Biol. 2006. Vol. 8. N 1. P. 91—99.; Smerdon M.J. DNA repair and the role of chromatin structure // Curr. Opin. Cell Biol. 1991. Vol. 3. N 3. P. 422—428.; Gospodinov A., Herceg Z. Shaping chromatin for repair // Mutat. Res. 2013. Vol. 752. N 1. P. 45—60.; Mandemaker I.K., Vermeulen W., Marteijn J.A. Gearing up chromatin: A role for chromatin remodeling during the transcriptional restart upon DNA damage // Nucleus. 2014. Vol. 5. N 3. P. 203—210.; Bird A.W., Yu D.Y., Pray-Grant M.G., Qiu Q., Harmon K.E., Megee P.C., Grant P.A., Smith M.M., Christman M.F. Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair // Nature. 2002. Vol. 419. N 6905. P. 411—415.; Downs J.A., Allard S., Jobin-Robitaille O., Javaheri A., Auger A., Bouchard N., Kron S.J., Jackson S.P., Cote J. Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites // Mol. Cell. 2004. Vol. 16. N 6. P. 979—990.; Fousteri M., Mullenders L.H. Transcription-coupled nucleotide excision repair in mammalian cells: molecular mechanisms and biological effects // Cell Res. 2008. Vol. 18. N 1. P. 73—84.; van Attikum H., Gasser S.M. The histone code at DNA breaks: a guide to repair? // Nat. Rev. Mol. Cell Biol. 2005. Vol. 6. N 10. P. 757—765.; Soria G., Polo S.E., Almouzni G. Prime, repair, restore: the active role of chromatin in the DNA damage response // Mol. Cell. 2012. Vol. 47. N 4. P. 497—510.; Downey M., Durocher D. Chromatin and DNA repair: the benefits of relaxation // Nat. Cell Biol. 2006. Vol. 8. N 1. P. 9—10.; Khurana S., Kruhlak M.J., Kim J., Tran A.D., Liu J., Nyswaner K., Shi L., Jailwala P., Sung M.H., Hakim O., Oberdoerffer P. A macrohistone variant links dynamic chromatin compaction to BRCA1-dependent genome maintenance // Cell Rep. 2014. Vol. 8. N 4. P. 1049—1062.; Li M.L., Yuan G., Greenberg R.A. Chromatin yo-yo: expansion and condensation during DNA repair // Trends Cell Biol. 2014. Vol. 24. N 11. P. 616—618.; Keogh M.C., Kim J.A., Downey M. A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery // Nature. 2006. Vol. 439. N 7075. P. 497—501.; Kusch T., Florens L., Macdonald W.H., Swanson S.K., Glaser R.L., Yates J.R. 3rd, Abmayr S.M., Washburn M.P., Workman J.L. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions // Science. 2004. Vol. 306. N 5704. P. 2084—2087.; Laugel V. Cockayne syndrome: the expanding clinical and mutational spectrum // Mech. Ageing Dev. 2013. Vol. 134. N 5—6. P. 161—170.; Adam S., Polo S.E., Almouzni G. Transcription recovery after DNA damage requires chromatin priming by the H3.3 histone chaperone HIRA // Cell. 2013. Vol. 155. N 1. P. 94—106.; Dinant C., Ampatziadis-Michailidis G., Lans H., Tresini M., Lagarou A., Grosbart M., Theil A.F., van Cappellen W.A., Kimura H., Bartek J., Fousteri M., Houtsmuller A.B., Vermeulen W., Marteijn J.A. Enhanced chromatin dynamics by FACT promotes transcriptional restart after UV-induced DNA damage // Mol. Cell. 2013. Vol. 51. N 4. P. 469—79.; Oksenych V., Zhovmer A., Ziani S., Mari P.O., Eberova J., Nardo T., Stefanini M., Giglia-Mari G., Egly J.M., Coin F. Histone methyltransferase DOT1L drives recovery of gene expression after a genotoxic attack // PLoS Genet. 2013. Vol. 9. N 7. P. e1003611.; Szenker E., Lacoste N., Almouzni G. A developmental requirement for HIRA-dependent H3.3 deposition revealed at gastrulation in Xenopus // Cell Rep. 2012. Vol. 1. N 6. P. 730—740.; Wilson M.D., Harreman M., Svejstrup J.Q. 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Availability: https://vestnik-bio-msu.elpub.ru/jour/article/view/269
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6Academic Journal
Authors: V. M. Studitsky, I. V. Orlovsky, O. V. Chertkov, N. S. Efimova, M. A. Loginova, O. I. Kulaeva, В. М. Студитский, И. В. Орловский, О. В. Чертков, Н. С. Ефимова, М. А. Логинова, О. И. Кулаева
Source: Vestnik Moskovskogo universiteta. Seriya 16. Biologiya; № 4 (2012); 10-16 ; Вестник Московского университета. Серия 16. Биология; № 4 (2012); 10-16 ; 0137-0952 ; 10.1234/XXXX-XXXX-2012-4
Subject Terms: РНК-полимераза 3, transcription, nucleosome, nucleosome barrier, chromatin remodeling, elongation, RNA polymerase III, транскрипция, нуклеосома, “нуклеосомный барьер”, ремоделирование хроматина, элонгация
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Relation: https://vestnik-bio-msu.elpub.ru/jour/article/view/68/70; Bednar J., Studitsky V.M., Grigoryev S.A., Felsenfeld G., Woodcock C.L. The nature of the nucleosomal barrier to transcription: direct observation of paused intermediates by electron cryomicroscopy // Mol. Cell. 1999. Vol. 4. N 3. P. 377—386.; Studitsky V.M., Kassavetis G.A., Geiduschek E.P., Felsenfeld G. Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase // Science. 1997. Vol. 278. N 5345. P. 1960—1963.; Gangaraju V.K., Bartholomew B. Mechanisms of ATP dependent chromatin remodeling // Mutat. Res. 2007. Vol. 618. N 1—2. P. 3—17.; Cairns B.R. Chromatin remodeling: insights and intrigue from single-molecule studies // Nat. Struct. Mol. Biol. 2007. Vol. 14. N 11. P. 989—996.; Studitsky V.M., Clark D.J., Felsenfeld G. A histone octamer can step around a transcribing polymerase without leaving the template // Cell. 1994. Vol. 76. N 2. P. 371—382.; Oler A.J., Alla R.K., Roberts D.N., Wong A., Hollenhorst P.C., Chandler K.J., Cassiday P.A., Nelson C.A., Hagedorn C.H., Graves B.J., Cairns B.R. Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors // Nat. Struct. Mol. Biol. 2010. Vol. 17. N 5. P. 620—628.; Kireeva M.L., Walter W., Tchernajenko V., Bondarenko V., Kashlev M., Studitsky V.M. Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription // Mol. Cell. 2002. Vol. 9. N 3. P. 541—552.; Kulaeva O.I., Gaykalova D.A., Pestov N.A., Golovastov V.V., Vassylyev D.G., Artsimovitch I., Studitsky V.M. Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II // Nat. Struct. Mol. Biol. 2009. Vol. 16. N 12. P. 1272—1278.
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7Academic Journal
Authors: V. M. Studitsky, I. V. Orlovsky, O. V. Chertkov, N. S. Efimova, M. A. Loginova, O. I. Kulaeva, В. М. Студитский, И. В. Орловский, О. В. Чертков, Н. С. Ефимова, М. А. Логинова, О. И. Кулаева
Source: Vestnik Moskovskogo universiteta. Seriya 16. Biologiya; № 3 (2012); 6-11 ; Вестник Московского университета. Серия 16. Биология; № 3 (2012); 6-11 ; 0137-0952
Subject Terms: РНК-полимераза 3, transcription, elongation, nucleosome, RNA polymerase III, транскрипция, элонгация, нуклеосома
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Relation: https://vestnik-bio-msu.elpub.ru/jour/article/view/57/59; Borukhov S., Nudler E. RNA polymerase: the vehicle of transcription // Trends Microbiol. 2008. Vol. 16. N 3. P. 126—134.; Davey C.A., Sargent D.F., Luger K., Maeder A.W., Richmond T.J. Solvent mediated interactions in the structure of the nucleosome core particle at 1,9 a resolution // J. Mol. Biol. 2002. Vol. 319. N 5. P. 1097—1113.; Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J. Crystal structure of the nucleosome core particle at 2,8 A resolution // Nature. 1997. Vol. 389. N 6648. P. 251—260.; Syed S.H., Goutte-Gattat D., Becker N., Meyer S., Shukla M.S., Hayes J.J., Everaers R., Angelov D., Bednar J., Dimitrov S. Single-base resolution mapping of H1-nucleosome interactions and 3D organization of the nucleosome // Proc. Natl. Acad. Sci. USA. 2010. Vol. 107. N 21. P. 9620—9625.; Schalch T., Duda S., Sargent D.F., Richmond T.J. X-ray structure of a tetranucleosome and its implications for the chromatin fibre // Nature. 2005. Vol. 436. N 7047. P. 138—141.; Routh A., Sandin S., Rhodes D. Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure // Proc. Natl. Acad. Sci. USA. 2008. Vol. 105. N 26. P. 8872—8877.; Fraser P., Bickmore W. Nuclear organization of the genome and the potential for gene regulation // Nature. 2007. Vol. 447. N 7143. P. 413—417.; Martens J.A., Wu P.Y., Winston F. Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae // Genes Dev. 2005. Vol. 19. N 22. P. 2695—2704.; Feser J., Truong D., Das C., Carson J.J., Kieft J., Harkness T., Tyler J.K. Elevated histone expression promotes life span extension // Mol. Cell. 2010. Vol. 39. N 5. P. 724—735.; Chi P., Allis C.D., Wang G.G. Covalent histone modifications-miswritten, misinterpreted and mis-erased in human cancers // Nat. Rev. Cancer. 2010. Vol. 10. N 7. P. 457—469.; Studitsky V.M., Clark D.J., Felsenfeld G. A histone octamer can step around a transcribing polymerase without leaving the template // Cell. 1994. Vol. 76. N 2. P. 371—382.; Mavrich T.N., Jiang C., Ioshikhes I.P., Li X., Venters B.J., Zanton S.J., Tomsho L.P., Qi J., Glaser R.L., Schuster S.C., Gilmour D.S., Albert I., Pugh B.F. Nucleosome organization in the Drosophila genome // Nature. 2008. Vol. 453. N 7193. P. 358—362.; Bednar J., Studitsky V.M., Grigoryev S.A., Felsenfeld G., Woodcock C.L. The nature of the nucleosomal barrier to transcription: direct observation of paused intermediates by electron cryomicroscopy // Mol. Cell. 1999. Vol. 4. N 3. P. 377—386.; Studitsky V.M., Clark D.J., Felsenfeld G. Overcoming a nucleosomal barrier to transcription // Cell. 1995. Vol. 83. N 1. P. 19—27.
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8Academic Journal
Authors: K. S. Kudryashova, D. V. Nikitin, O. V. Chertkov, N. S. Gerasimova, M. E. Valieva, V. M. Studitsky, A. V. Feofanov, К. С. Кудряшова, Д. В. Никитин, О. В. Чертков, Н. С. Герасимова, М. Е. Валиева, В. М. Студитский, А. В. Феофанов
Source: Vestnik Moskovskogo universiteta. Seriya 16. Biologiya; № 4 (2015); 41-45 ; Вестник Московского университета. Серия 16. Биология; № 4 (2015); 41-45 ; 0137-0952
Subject Terms: эпигенетика, RNA polymerase, fluorescence, microscopy, epigenetics, РНК-полимераза, флуоресценция, микроскопия
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Relation: https://vestnik-bio-msu.elpub.ru/jour/article/view/282/280; Luger K., Mäder A.W., Richmond R.K., Sargent D.F., Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 Ǻ resolution // Nature. 1997. Vol. 389. N 6648. P. 251–260.; Chang H.W., Kulaeva O.I., Shaytan A.K., Kibanov M., Kuznedelov K., Severinov K.V., Kirpichnikov M.P., Clark D.J., Studitsky V.M. Analysis of the mechanism of nucleosome survival during transcription // Nucleic Acids Res. 2014. Vol. 42. N 3. P. 1619–1627.; Chang H.W., Shaytan A.K., Hsieh F.-K., Kulaeva O.I., Kirpichnikov M.P, Studitsky V.M. Structural analysis of the key intermediate formed during transcription through a nucleosome // Trends Cell. Mol. Biol. 2013. Vol. 8. P. 13–23.; Walter W., Studitsky V.M. Construction, analysis, and transcription of model nucleosomal templates // Methods. 2004. Vol. 33. N 1. P. 18–24.; Gaykalova D.A., Kulaeva O.I., Bondarenko V.A., Studitsky V.M. Preparation and analysis of uniquely positioned mononucleosomes // Methods Mol. Biol. 2009. Vol. 523. P. 109–123.; Gaykalova D.A., Kulaeva O.I., Pestov N.A., Hsieh F.K., Studitsky V.M. Experimental analysis of the mechanism of chromatin remodeling by RNA polymerase II // Methods Enzymol. 2012. Vol. 512. P. 293–314.; Buning R., van Noort J. Single-pair FRET experiments on nucleosome conformational dynamics // Biochimie. 2010. Vol. 92. N 12. P. 1729–1740.; Choy J.S., Lee T.H. Structural dynami cs of nucleosomes at single-molecule resolution // Trends Biochem. Sci. 2012. Vol. 37. N 10. P. 425–435.; Walter W., Kireeva M.L., Tchernajenko V., Kashlev M., Studitsky V.M. Assay of the fate of the nucleosome during transcription by RNA polymerase II // Methods Enzymol. 2003. Vol. 371. P. 564–577.; Kulaeva O.I., Gaykalova D.A., Pestov N.A., Golovastov V.V., Vassylyev D.G., Artsimovitch I., Studitsky V.M. Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II // Nat. Struct. Mol. Biol. 2009. Vol. 16. N 12. P. 1272–1278.; Kireeva M.L., Walter W., Tchernajenko V., Bondarenko V., Kashlev M., Studitsky V.M. Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription // Mol. Cell. 2002. Vol. 9. N 3. P. 541–552.
Availability: https://vestnik-bio-msu.elpub.ru/jour/article/view/282
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9Academic Journal
Authors: Кабанов, Игорь, Никитина, Татьяна, Тищенко, Людмила
Subject Terms: ГЕНЫ КЛАССА III, РНК-ПОЛИМЕРАЗА III, СТАБИЛЬНЫЕ НЕТРАНСЛИРУЕМЫЕ РНК, SINE-ПОСЛЕДОВАТЕЛЬНОСТИ, ALU-ПОВТОРЫ, ОТ-ПЦР В РЕАЛЬНОМ ВРЕМЕНИ, МЕТИЛИРОВАНИЕ ДНК, АПОПТОЗ
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10Academic Journal
Authors: Матусевич, Олег, Глуздиков, Иван, Титов, Михаил
Subject Terms: СИНТЕЗ ПЕПТИДОВ, ВИРУСЫ ГРИППА А, РНК-ПОЛИМЕРАЗА
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11Academic Journal
Authors: Никитина, Татьяна, Гао, Л., Карпачева, Клавдия, Тищенко, Людмила
Subject Terms: ГЕНЫ КЛАССА III, РНК-ПОЛИМЕРАЗА III, СТАБИЛЬНЫЕ НЕТРАНСЛИРУЕМЫЕ РНК, SINE-ПОСЛЕДОВАТЕЛЬНОСТИ, ОТ-ПЦР В РЕАЛЬНОМ ВРЕМЕНИ, МЕТИЛИРОВАНИЕ ДНК, АПОПТОЗ
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12Academic Journal
Source: Вестник Новгородского государственного университета им. Ярослава Мудрого.
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13Academic Journal
Source: Вестник Санкт-Петербургского университета. Серия 3. Биология.
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14Academic Journal
Source: Вестник Санкт-Петербургского университета. Серия 4. Физика. Химия.
Subject Terms: СИНТЕЗ ПЕПТИДОВ, ВИРУСЫ ГРИППА А, РНК-ПОЛИМЕРАЗА, 3. Good health
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15Academic Journal
Source: Вестник Санкт-Петербургского университета. Серия 3. Биология.
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16Academic Journal
Authors: Омарова Х.Г., Балыкова Л.А., Пшеничная Н.Ю., Земсков Д.Н., Заславская К.Я., Таганов А.В., Белый П.А.
Source: Infektsionnye Bolezni
Subject Terms: RNA-dependent RNA polymerase (RdRp), favipiravir, molnupiravir, covid-19, SARS-CoV-2, РНК-зависимая РНК-полимераза (RdRp), фавипиравир, молнупиравир
Availability: https://repository.rudn.ru/records/article/record/98018/
