Coding

Part:BBa_K5492401:Design

Designed by: Norbert Nyeste   Group: iGEM24_TERMOSZ-Selye-HUN   (2024-09-10)
Revision as of 17:03, 26 September 2024 by Simonkasara (Talk | contribs) (→‎Design Notes)


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.