Difference between revisions of "Part:BBa K2675097:Design"

 
 
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===Design Notes===
 
===Design Notes===
−
selection from a random sequence library
+
pAimX(full) promoter of phage phi3T ([[Part:BBa_K2675020|BBa_K2675020]]) with mutations in the putative terminator. These mutations disrupted also the pAimX(2) and pAimX(3) putative promoters.
−
 
+
−
 
+
  
 
===Source===
 
===Source===
  
−
selection from a random sequence library
+
selection from a random sequence library derived by PCR with degenerate primers on [[Part:BBa_K2675057|BBa_K2675057]].
  
 
===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] 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.

Latest revision as of 23:00, 17 October 2018


pAimX(full-noTerminator-v8) promoter 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
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 71


Design Notes

pAimX(full) promoter of phage phi3T (BBa_K2675020) with mutations in the putative terminator. These mutations disrupted also the pAimX(2) and pAimX(3) putative promoters.

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.