Difference between revisions of "Part:BBa K5492401:Design"

 
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===Design Notes===
 
===Design Notes===
−
Codon optimisation for the following codons: AGA -> CGT, AGG -> CGT, ATA -> ATC, CCC -> CCG, CGG -> GCT, CTA -> CTG, GGA -> GGC,  TCC -> TCT, CTC -> CTG, CCA -> CCG, CTT -> CTG, GGG -> GGC, CCT -> CCG, GCC -> GCT
+
Codon optimisation for E.coli:
−
 
+
  
 +
Position  Changes
 +
10        TCC -> TCT
 +
16        AGG -> CGT
 +
58        CGG -> CGT
 +
61        AGG -> CGT
 +
67        CTC -> CTG
 +
76        TCC -> TCT
 +
121      CCA -> CCG
 +
127      ATA -> ATC
 +
130      ATA -> ATC
 +
136      AGG -> CGT
 +
175      ATA -> ATC
 +
202      CTT -> CTG
 +
211      CTC -> CTG
 +
214      TCC -> TCT
 +
235      CCA -> CCG
 +
268      CCA -> CCG
 +
286      GCC -> GCT
 +
301      CTT -> CTG
 +
307      GCC -> GCT
 +
322      CTC -> CTG
 +
376      AGA -> CGT
 +
397      CTT -> CTG
 +
454      CCA -> CCG
 +
481      CTC -> CTG
 +
484      TTA -> CTG
 +
505      CTC -> CTG
 +
571      CCC -> CCG
 +
583      CTC -> CTG
 +
610      CTC -> CTG
 +
634      GGG -> GGC
 +
637      CTT -> CTG
 +
658      CTT -> CGG
 +
664      TCC -> TCT
 +
711      A  -> C
 +
715      CTT -> CTG
 +
754      GCC -> GCT
 +
763      CCA -> CCG
 +
766      CCT -> CCG
 +
772      CTC -> CTG
 +
775      AGA -> CGT
 +
784      CTT -> CTG
 +
787      GGG -> GGC
 +
805      CCT -> CCG
 +
829      GGG -> GGC
 +
838      CTT -> CTG
 +
862      ATA -> ATC
  
 
===Source===
 
===Source===
  
−
https://www.ncbi.nlm.nih.gov/nuccore/AH003685 , Part BBa_K5492400 (https://parts.igem.org/Part:BBa_K5492400)
+
https://www.ncbi.nlm.nih.gov/nuccore/AH003685, [https://parts.igem.org/Part:BBa_K5492400 BBa_K5492400], https://www.genscript.com/gentitan-gene-fragments.html
  
 
===References===
 
===References===
 +
Dong H, Nilsson L, Kurland CG. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol. 1996 Aug 2;260(5):649-63. doi: 10.1006/jmbi.1996.0428. PMID: 8709146.
 +
 +
Lipinszki Z, Vernyik V, Farago N, Sari T, Puskas LG, Blattner FR, Posfai G, Gyorfy Z. Enhancing the Translational Capacity of E. coli by Resolving the Codon Bias. ACS Synth Biol. 2018 Nov 16;7(11):2656-2664. doi: 10.1021/acssynbio.8b00332. Epub 2018 Nov 2. PMID: 30351909.

Latest revision as of 07:03, 2 October 2024


Optimised Human Histamine-N-Methlytransferase - HNMT


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 100
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 100
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 100
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 100
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 100
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Codon optimisation for E.coli: 

Position  Changes 
10        TCC -> TCT
16        AGG -> CGT
58        CGG -> CGT
61        AGG -> CGT
67        CTC -> CTG
76        TCC -> TCT
121       CCA -> CCG
127       ATA -> ATC
130       ATA -> ATC
136       AGG -> CGT
175       ATA -> ATC
202       CTT -> CTG
211       CTC -> CTG
214       TCC -> TCT
235       CCA -> CCG
268       CCA -> CCG
286       GCC -> GCT
301       CTT -> CTG
307       GCC -> GCT
322       CTC -> CTG
376       AGA -> CGT
397       CTT -> CTG
454       CCA -> CCG
481       CTC -> CTG
484       TTA -> CTG
505       CTC -> CTG
571       CCC -> CCG
583       CTC -> CTG
610       CTC -> CTG
634       GGG -> GGC
637       CTT -> CTG
658       CTT -> CGG
664       TCC -> TCT
711       A   -> C
715       CTT -> CTG
754       GCC -> GCT
763       CCA -> CCG
766       CCT -> CCG
772       CTC -> CTG
775       AGA -> CGT
784       CTT -> CTG
787       GGG -> GGC
805       CCT -> CCG
829       GGG -> GGC
838       CTT -> CTG
862       ATA -> ATC

Source

https://www.ncbi.nlm.nih.gov/nuccore/AH003685, BBa_K5492400, https://www.genscript.com/gentitan-gene-fragments.html

References

Dong H, Nilsson L, Kurland CG. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol. 1996 Aug 2;260(5):649-63. doi: 10.1006/jmbi.1996.0428. PMID: 8709146.

Lipinszki Z, Vernyik V, Farago N, Sari T, Puskas LG, Blattner FR, Posfai G, Gyorfy Z. Enhancing the Translational Capacity of E. coli by Resolving the Codon Bias. ACS Synth Biol. 2018 Nov 16;7(11):2656-2664. doi: 10.1021/acssynbio.8b00332. Epub 2018 Nov 2. PMID: 30351909.