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

(→‎Design Notes)
(→‎Design Notes)
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===Design Notes===
 
===Design Notes===
−
Codon optimisation for e. coli chassis.
+
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===

Revision as of 16:58, 26 September 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

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.