[{"page":"475-484","date_created":"2020-08-30T22:01:11Z","publication":"Molecular Biology","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"FyKo"}],"article_processing_charge":"No","article_type":"original","external_id":{"isi":["000562110300001"]},"quality_controlled":"1","volume":54,"related_material":{"record":[{"id":"8321","status":"public","relation":"original"}]},"acknowledgement":"We would like to thank our co-workers and members of the Alkalaeva lab for participating in discussions about the topics covered in this essay.","day":"19","author":[{"last_name":"Mukba","first_name":"S. A.","full_name":"Mukba, S. A."},{"first_name":"Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","last_name":"Vlasov","full_name":"Vlasov, Petr"},{"full_name":"Kolosov, P. M.","last_name":"Kolosov","first_name":"P. M."},{"full_name":"Shuvalova, E. Y.","last_name":"Shuvalova","first_name":"E. Y."},{"full_name":"Egorova, T. V.","first_name":"T. V.","last_name":"Egorova"},{"first_name":"E. Z.","last_name":"Alkalaeva","full_name":"Alkalaeva, E. Z."}],"isi":1,"publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Expanding the genetic code: Unnatural base pairs in biological systems","publication_status":"published","doi":"10.1134/S0026893320040111","oa_version":"None","date_published":"2020-08-19T00:00:00Z","scopus_import":"1","intvolume":"        54","citation":{"chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” <i>Molecular Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1134/S0026893320040111\">https://doi.org/10.1134/S0026893320040111</a>.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., &#38; Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1134/S0026893320040111\">https://doi.org/10.1134/S0026893320040111</a>","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 54(4), 475–484.","mla":"Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” <i>Molecular Biology</i>, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:<a href=\"https://doi.org/10.1134/S0026893320040111\">10.1134/S0026893320040111</a>.","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” <i>Molecular Biology</i>, vol. 54, no. 4. Springer Nature, pp. 475–484, 2020.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molecular Biology</i>. 2020;54(4):475-484. doi:<a href=\"https://doi.org/10.1134/S0026893320040111\">10.1134/S0026893320040111</a>","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484."},"date_updated":"2023-08-22T09:01:03Z","issue":"4","abstract":[{"text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications.","lang":"eng"}],"year":"2020","_id":"8320","status":"public","publication_identifier":{"issn":["00268933"],"eissn":["16083245"]},"month":"08"},{"related_material":{"record":[{"id":"8320","relation":"translation","status":"public"}]},"volume":54,"quality_controlled":"1","external_id":{"pmid":["32799218"]},"article_processing_charge":"No","article_type":"original","department":[{"_id":"FyKo"}],"language":[{"iso":"rus"}],"type":"journal_article","publication":"Molekuliarnaia biologiia","page":"531-541","date_created":"2020-08-30T22:01:11Z","title":"Expanding the genetic code: Unnatural base pairs in biological systems","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publisher":"Russian Academy of Sciences","author":[{"first_name":"S. A.","last_name":"Mukba","full_name":"Mukba, S. A."},{"full_name":"Vlasov, Petr","first_name":"Petr","last_name":"Vlasov","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kolosov","first_name":"P. M.","full_name":"Kolosov, P. M."},{"full_name":"Shuvalova, E. Y.","last_name":"Shuvalova","first_name":"E. Y."},{"last_name":"Egorova","first_name":"T. V.","full_name":"Egorova, T. V."},{"first_name":"E. Z.","last_name":"Alkalaeva","full_name":"Alkalaeva, E. Z."}],"day":"01","pmid":1,"citation":{"chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological systems.” <i>Molekuliarnaia biologiia</i>. Russian Academy of Sciences, 2020. <a href=\"https://doi.org/10.31857/S0026898420040126\">https://doi.org/10.31857/S0026898420040126</a>.","mla":"Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in biological systems.” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 4, Russian Academy of Sciences, 2020, pp. 531–41, doi:<a href=\"https://doi.org/10.31857/S0026898420040126\">10.31857/S0026898420040126</a>.","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 54(4), 531–541.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., &#38; Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molekuliarnaia biologiia</i>. Russian Academy of Sciences. <a href=\"https://doi.org/10.31857/S0026898420040126\">https://doi.org/10.31857/S0026898420040126</a>","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 531–541.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molekuliarnaia biologiia</i>. 2020;54(4):531-541. doi:<a href=\"https://doi.org/10.31857/S0026898420040126\">10.31857/S0026898420040126</a>","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020."},"intvolume":"        54","scopus_import":"1","date_published":"2020-07-01T00:00:00Z","oa_version":"None","doi":"10.31857/S0026898420040126","publication_status":"published","month":"07","publication_identifier":{"issn":["00268984"]},"status":"public","_id":"8321","year":"2020","issue":"4","abstract":[{"lang":"eng","text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications."}],"date_updated":"2023-08-22T09:01:02Z"},{"publication":"Molecular Biology","page":"739-748","date_created":"2020-10-25T23:01:17Z","department":[{"_id":"FyKo"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","article_type":"original","related_material":{"record":[{"id":"8701","status":"public","relation":"original"}]},"volume":54,"quality_controlled":"1","external_id":{"isi":["000579441200009"]},"day":"01","acknowledgement":"We would like to thank the staff of CCU Genome for sequencing, Tat’yana Pestova, Christopher Helen, and Lyudmila Yur’evna Frolova for the plasmids provided, as well as the laboratory staff for productive discussion of the results. We also thank former laboratory employees Yuliya Vladimirovna Bocharova and Polina Nikolaevna Kryuchkova for the exceptional contribution to the present work.","isi":1,"author":[{"last_name":"Sokolova","first_name":"E. E.","full_name":"Sokolova, E. E."},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","last_name":"Vlasov","first_name":"Petr","full_name":"Vlasov, Petr"},{"first_name":"T. V.","last_name":"Egorova","full_name":"Egorova, T. V."},{"full_name":"Shuvalov, A. V.","first_name":"A. V.","last_name":"Shuvalov"},{"last_name":"Alkalaeva","first_name":"E. Z.","full_name":"Alkalaeva, E. Z."}],"title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","doi":"10.1134/S0026893320050088","publication_status":"published","date_published":"2020-09-01T00:00:00Z","oa_version":"None","scopus_import":"1","intvolume":"        54","citation":{"ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. <i>Molecular Biology</i>. 2020;54(5):739-748. doi:<a href=\"https://doi.org/10.1134/S0026893320050088\">10.1134/S0026893320050088</a>","ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” <i>Molecular Biology</i>, vol. 54, no. 5. Springer Nature, pp. 739–748, 2020.","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular Biology 54 (2020) 739–748.","mla":"Sokolova, E. E., et al. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” <i>Molecular Biology</i>, vol. 54, no. 5, Springer Nature, 2020, pp. 739–48, doi:<a href=\"https://doi.org/10.1134/S0026893320050088\">10.1134/S0026893320050088</a>.","ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 54(5), 739–748.","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., &#38; Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. <i>Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1134/S0026893320050088\">https://doi.org/10.1134/S0026893320050088</a>","chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” <i>Molecular Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1134/S0026893320050088\">https://doi.org/10.1134/S0026893320050088</a>."},"year":"2020","issue":"5","abstract":[{"lang":"eng","text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency."}],"date_updated":"2023-08-22T10:39:38Z","_id":"8700","publication_identifier":{"issn":["00268933"],"eissn":["16083245"]},"status":"public","month":"09"},{"date_updated":"2023-08-22T10:39:37Z","abstract":[{"lang":"eng","text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency."}],"issue":"5","year":"2020","_id":"8701","status":"public","publication_identifier":{"issn":["00268984"]},"month":"09","publication_status":"published","doi":"10.31857/S0026898420050080","oa_version":"None","date_published":"2020-09-01T00:00:00Z","scopus_import":"1","intvolume":"        54","citation":{"ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 5. Russian Academy of Sciences, pp. 837–848, 2020.","ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. <i>Molekuliarnaia biologiia</i>. 2020;54(5):837-848. doi:<a href=\"https://doi.org/10.31857/S0026898420050080\">10.31857/S0026898420050080</a>","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 837–848.","mla":"Sokolova, E. E., et al. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 5, Russian Academy of Sciences, 2020, pp. 837–48, doi:<a href=\"https://doi.org/10.31857/S0026898420050080\">10.31857/S0026898420050080</a>.","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., &#38; Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. <i>Molekuliarnaia biologiia</i>. Russian Academy of Sciences. <a href=\"https://doi.org/10.31857/S0026898420050080\">https://doi.org/10.31857/S0026898420050080</a>","ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 54(5), 837–848.","chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” <i>Molekuliarnaia biologiia</i>. Russian Academy of Sciences, 2020. <a href=\"https://doi.org/10.31857/S0026898420050080\">https://doi.org/10.31857/S0026898420050080</a>."},"pmid":1,"day":"01","author":[{"full_name":"Sokolova, E. E.","last_name":"Sokolova","first_name":"E. E."},{"full_name":"Vlasov, Petr","last_name":"Vlasov","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"full_name":"Egorova, T. V.","first_name":"T. V.","last_name":"Egorova"},{"full_name":"Shuvalov, A. V.","last_name":"Shuvalov","first_name":"A. V."},{"full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva","first_name":"E. Z."}],"publisher":"Russian Academy of Sciences","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","page":"837-848","date_created":"2020-10-25T23:01:17Z","publication":"Molekuliarnaia biologiia","type":"journal_article","language":[{"iso":"rus"}],"department":[{"_id":"FyKo"}],"article_processing_charge":"No","article_type":"original","external_id":{"pmid":["33009793"]},"volume":54,"quality_controlled":"1","related_material":{"record":[{"relation":"translation","status":"public","id":"8700"}]}}]