Difference between revisions of "Part:BBa K2675196:Design"

 
 
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===Design Notes===
 
===Design Notes===
−
BBa_J23110 BBa_K2675071 BBa_K2675096 BBa_K2675016 BBa_K2675006 BBa_K2675030
+
[[Part:BBa_J23110|BBa_J23110]] constitutive promoter + pAimX(full-noTerminator-v7) promoter ([[Part:BBa_K2675096|BBa_K2675096]]) + custom made RBS ([[Part:BBa_K2675016|BBa_K2675016]]) + sfGFP-LVAtag coding sequence ([[Part:BBa_K2675006|BBa_K2675006]]) + the strong L3S2P56 Terminator ([[Part:BBa_K2675030|BBa_K2675030]])
  
 +
===Source===
  
 +
selection from a random sequence library derived by PCR with degenerate primers on [[Part:BBa_K2675057|BBa_K2675057]].
  
−
===Source===
+
===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] Solovyev V, Salamov A. Automatic Annotation of Microbial Genomes and Metagenomic Sequences. In Metagenomics and its Applications in Agriculture, Biomedicine and Environmental Studies (Ed. R.W. Li), Nova Science Publishers (2011) p. 61-78.
  
 +
[3] Gautheret D, Lambert A. Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J Mol Biol (2001) 313, 1003-1011.
  
 +
[4] Macke T, Ecker D, Gutell R, Gautheret D, Case DA and Sampath R. RNAMotif – A new RNA secondary structure definition and discovery algorithm. Nucleic Acids Res (2001) 29, 4724–4735.
  
−
===References===
+
[5] Chen YJ, Liu P, Nielsen AA, Brophy JA, Clancy K, Peterson T, Voigt CA. Characterization of 582 natural and synthetic terminators and quantification of their design constraints. Nat Methods (2013) 10, 659-664.
 +
 
 +
[6] Herskowitz I, Hagen D. The lysis-lysogeny decision of phage lambda: explicit programming and responsiveness. Annu Rev Genet (1980) 14, 399-445.

Latest revision as of 23:02, 17 October 2018


sfGFP-LVAtag expression cassette under the control of J23110 and pAimX(full-noTerminator-v7) promote


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 7
    Illegal NheI site found at 30
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 233
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 104


Design Notes

BBa_J23110 constitutive promoter + pAimX(full-noTerminator-v7) promoter (BBa_K2675096) + custom made RBS (BBa_K2675016) + sfGFP-LVAtag coding sequence (BBa_K2675006) + the strong L3S2P56 Terminator (BBa_K2675030)

Source

selection from a random sequence library derived by PCR with degenerate primers on BBa_K2675057.

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] Solovyev V, Salamov A. Automatic Annotation of Microbial Genomes and Metagenomic Sequences. In Metagenomics and its Applications in Agriculture, Biomedicine and Environmental Studies (Ed. R.W. Li), Nova Science Publishers (2011) p. 61-78.

[3] Gautheret D, Lambert A. Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J Mol Biol (2001) 313, 1003-1011.

[4] Macke T, Ecker D, Gutell R, Gautheret D, Case DA and Sampath R. RNAMotif – A new RNA secondary structure definition and discovery algorithm. Nucleic Acids Res (2001) 29, 4724–4735.

[5] Chen YJ, Liu P, Nielsen AA, Brophy JA, Clancy K, Peterson T, Voigt CA. Characterization of 582 natural and synthetic terminators and quantification of their design constraints. Nat Methods (2013) 10, 659-664.

[6] Herskowitz I, Hagen D. The lysis-lysogeny decision of phage lambda: explicit programming and responsiveness. Annu Rev Genet (1980) 14, 399-445.