---
_id: '8320'
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.
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.
article_processing_charge: No
article_type: original
author:
- first_name: S. A.
  full_name: Mukba, S. A.
  last_name: Mukba
- first_name: Petr
  full_name: Vlasov, Petr
  id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
  last_name: Vlasov
- first_name: P. M.
  full_name: Kolosov, P. M.
  last_name: Kolosov
- first_name: E. Y.
  full_name: Shuvalova, E. Y.
  last_name: Shuvalova
- first_name: T. V.
  full_name: Egorova, T. V.
  last_name: Egorova
- first_name: E. Z.
  full_name: Alkalaeva, E. Z.
  last_name: Alkalaeva
citation:
  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>'
  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>'
  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>.'
  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.'
  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>.'
  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_created: 2020-08-30T22:01:11Z
date_published: 2020-08-19T00:00:00Z
date_updated: 2023-08-22T09:01:03Z
day: '19'
department:
- _id: FyKo
doi: 10.1134/S0026893320040111
external_id:
  isi:
  - '000562110300001'
intvolume: '        54'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa_version: None
page: 475-484
publication: Molecular Biology
publication_identifier:
  eissn:
  - '16083245'
  issn:
  - '00268933'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  record:
  - id: '8321'
    relation: original
    status: public
scopus_import: '1'
status: public
title: 'Expanding the genetic code: Unnatural base pairs in biological systems'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 54
year: '2020'
...
---
_id: '8321'
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.
article_processing_charge: No
article_type: original
author:
- first_name: S. A.
  full_name: Mukba, S. A.
  last_name: Mukba
- first_name: Petr
  full_name: Vlasov, Petr
  id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
  last_name: Vlasov
- first_name: P. M.
  full_name: Kolosov, P. M.
  last_name: Kolosov
- first_name: E. Y.
  full_name: Shuvalova, E. Y.
  last_name: Shuvalova
- first_name: T. V.
  full_name: Egorova, T. V.
  last_name: Egorova
- first_name: E. Z.
  full_name: Alkalaeva, E. Z.
  last_name: Alkalaeva
citation:
  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>'
  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>'
  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>.'
  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.'
  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.'
  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>.'
  short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva,
    Molekuliarnaia biologiia 54 (2020) 531–541.
date_created: 2020-08-30T22:01:11Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2023-08-22T09:01:02Z
day: '01'
department:
- _id: FyKo
doi: 10.31857/S0026898420040126
external_id:
  pmid:
  - '32799218'
intvolume: '        54'
issue: '4'
language:
- iso: rus
month: '07'
oa_version: None
page: 531-541
pmid: 1
publication: Molekuliarnaia biologiia
publication_identifier:
  issn:
  - '00268984'
publication_status: published
publisher: Russian Academy of Sciences
quality_controlled: '1'
related_material:
  record:
  - id: '8320'
    relation: translation
    status: public
scopus_import: '1'
status: public
title: 'Expanding the genetic code: Unnatural base pairs in biological systems'
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 54
year: '2020'
...
---
_id: '8700'
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.
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.
article_processing_charge: No
article_type: original
author:
- first_name: E. E.
  full_name: Sokolova, E. E.
  last_name: Sokolova
- first_name: Petr
  full_name: Vlasov, Petr
  id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
  last_name: Vlasov
- first_name: T. V.
  full_name: Egorova, T. V.
  last_name: Egorova
- first_name: A. V.
  full_name: Shuvalov, A. V.
  last_name: Shuvalov
- first_name: E. Z.
  full_name: Alkalaeva, E. Z.
  last_name: Alkalaeva
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>
  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>.
  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.
  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.
  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>.
  short: E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular
    Biology 54 (2020) 739–748.
date_created: 2020-10-25T23:01:17Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2023-08-22T10:39:38Z
day: '01'
department:
- _id: FyKo
doi: 10.1134/S0026893320050088
external_id:
  isi:
  - '000579441200009'
intvolume: '        54'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 739-748
publication: Molecular Biology
publication_identifier:
  eissn:
  - '16083245'
  issn:
  - '00268933'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  record:
  - id: '8701'
    relation: original
    status: public
scopus_import: '1'
status: public
title: The influence of A/G composition of 3' stop codon contexts on translation termination
  efficiency in eukaryotes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 54
year: '2020'
...
---
_id: '8701'
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.
article_processing_charge: No
article_type: original
author:
- first_name: E. E.
  full_name: Sokolova, E. E.
  last_name: Sokolova
- first_name: Petr
  full_name: Vlasov, Petr
  id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
  last_name: Vlasov
- first_name: T. V.
  full_name: Egorova, T. V.
  last_name: Egorova
- first_name: A. V.
  full_name: Shuvalov, A. V.
  last_name: Shuvalov
- first_name: E. Z.
  full_name: Alkalaeva, E. Z.
  last_name: Alkalaeva
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>Molekuliarnaia biologiia</i>. 2020;54(5):837-848. 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>
  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>.
  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.
  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.
  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>.
  short: E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia
    biologiia 54 (2020) 837–848.
date_created: 2020-10-25T23:01:17Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2023-08-22T10:39:37Z
day: '01'
department:
- _id: FyKo
doi: 10.31857/S0026898420050080
external_id:
  pmid:
  - '33009793'
intvolume: '        54'
issue: '5'
language:
- iso: rus
month: '09'
oa_version: None
page: 837-848
pmid: 1
publication: Molekuliarnaia biologiia
publication_identifier:
  issn:
  - '00268984'
publication_status: published
publisher: Russian Academy of Sciences
quality_controlled: '1'
related_material:
  record:
  - id: '8700'
    relation: translation
    status: public
scopus_import: '1'
status: public
title: The influence of A/G composition of 3' stop codon contexts on translation termination
  efficiency in eukaryotes
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 54
year: '2020'
...