Difference between revisions of "Part:BBa K2675000:Design"

 
 
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===Design Notes===
 
===Design Notes===
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This sequence has been specifically optimised for Escherichia coli K12 with the help of JCAT.
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This sequence has been specifically optimised for ''Escherichia coli'' K12 with the help of [http://www.jcat.de/ JCAT] based on the original phi3T AimR sequence ([[Part:BBa_K2279000|BBa_K2279000]]).
−
 
+
Before optimization, the CAI-Value of the original sequence was 0.1956 with a 32.4% GC-Content. The optimization allows a CAI-Value for the improved sequence of 0.8982 with a 44.1% GC-Content.
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+
  
 
===Source===
 
===Source===
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===References===
 
===References===
 +
[1] Erez Z, Steinberger-Levy I, Shamir M, Doron S, Stokar-Avihail A, Peleg Y, Melamed S, Leavitt A, Savidor A, Albeck S, Amitai G, Sorek R. Communication between viruses guides lysis-lysogeny decisions. Nature (2017) 541, 488-493.
 +
 +
[2] Dou C, Xiong J, Gu Y, Yin K, Wang J, Hu Y, Zhou D, Fu X, Qi S, Zhu X, Yao S, Xu H, Nie C, Liang Z, Yang S, Wei Y, Cheng W. Structural and functional insights into the regulation of the lysis-lysogeny decision in viral communities. Nat Microbiol (2018) doi: 10.1038/s41564-018-0259-7.
 +
 +
[3] Wang Q, Guan Z, Pei K, Wang J, Liu Z, Yin P, Peng D, Zou T. Structural basis of the arbitrium peptide-AimR communication system in the phage lysis-lysogeny decision. Nat Microbiol (2018) doi: 10.1038/s41564-018-0239-y.
 +
 +
[4] Espah Borujeni A, Channarasappa AS, Salis HM. Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids Res (2014) 42, 2646-2659.
 +
 +
[5] Salis HM, Mirsky EA, Voigt CA. Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol (2009) 27, 946-50.

Latest revision as of 03:24, 18 October 2018


AimR of phage phi3T


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

This sequence has been specifically optimised for Escherichia coli K12 with the help of [http://www.jcat.de/ JCAT] based on the original phi3T AimR sequence (BBa_K2279000). Before optimization, the CAI-Value of the original sequence was 0.1956 with a 32.4% GC-Content. The optimization allows a CAI-Value for the improved sequence of 0.8982 with a 44.1% GC-Content.

Source

DNA synthesis

References

[1] Erez Z, Steinberger-Levy I, Shamir M, Doron S, Stokar-Avihail A, Peleg Y, Melamed S, Leavitt A, Savidor A, Albeck S, Amitai G, Sorek R. Communication between viruses guides lysis-lysogeny decisions. Nature (2017) 541, 488-493.

[2] Dou C, Xiong J, Gu Y, Yin K, Wang J, Hu Y, Zhou D, Fu X, Qi S, Zhu X, Yao S, Xu H, Nie C, Liang Z, Yang S, Wei Y, Cheng W. Structural and functional insights into the regulation of the lysis-lysogeny decision in viral communities. Nat Microbiol (2018) doi: 10.1038/s41564-018-0259-7.

[3] Wang Q, Guan Z, Pei K, Wang J, Liu Z, Yin P, Peng D, Zou T. Structural basis of the arbitrium peptide-AimR communication system in the phage lysis-lysogeny decision. Nat Microbiol (2018) doi: 10.1038/s41564-018-0239-y.

[4] Espah Borujeni A, Channarasappa AS, Salis HM. Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids Res (2014) 42, 2646-2659.

[5] Salis HM, Mirsky EA, Voigt CA. Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol (2009) 27, 946-50.