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

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===Design Notes===
 
===Design Notes===
−
Codon optimisation in the following positions:
+
Codon optimisation for E.coli:
  
−
Start End note
+
Position  Changes
−
10 12 TCC -> TCT
+
10       TCC -> TCT
−
16 18 AGG -> CGT
+
16       AGG -> CGT
−
58 60 CGG -> CGT
+
58       CGG -> CGT
−
61 63 AGG-> CGT
+
61       AGG -> CGT
−
67 69 CTC -> CTG
+
67       CTC -> CTG
−
76 78 TCC -> TCT
+
76       TCC -> TCT
−
121 123 CCA -> CCG
+
121       CCA -> CCG
−
127 129 ATA -> ATC
+
127       ATA -> ATC
−
130 132 ATA -> ATC
+
130       ATA -> ATC
−
136 138 AGG -> CGT
+
136       AGG -> CGT
−
175 177 ATA -> ATC
+
175       ATA -> ATC
−
202 204 CTT -> CTG
+
202       CTT -> CTG
−
211 213 CTC -> CTG
+
211       CTC -> CTG
−
214 216 TCC -> TCT
+
214       TCC -> TCT
−
235 237 CCA -> CCG
+
235       CCA -> CCG
−
268 270 CCA -> CCG
+
268       CCA -> CCG
−
286 288 GCC -> GCT
+
286       GCC -> GCT
−
301 303 CTT -> CTG
+
301       CTT -> CTG
−
307 309 GCC -> GCT
+
307       GCC -> GCT
−
322 324 CTC -> CTG
+
322       CTC -> CTG
−
376 378 AGA -> CGT
+
376       AGA -> CGT
−
397 399 CTT -> CTG
+
397       CTT -> CTG
−
454 456 CCA -> CCG
+
454       CCA -> CCG
−
481 483 CTC -> CTG
+
481       CTC -> CTG
−
484 486 TTA - > CTG
+
484       TTA -> CTG
−
505 507 CTC -> CTG
+
505       CTC -> CTG
−
571 573 CCC -> CCG
+
571       CCC -> CCG
−
583 585 CTC -> CTG
+
583       CTC -> CTG
−
610 612 CTC -> CTG
+
610       CTC -> CTG
−
634 636 GGG -> GGC
+
634       GGG -> GGC
−
637 639 CTT -> CTG
+
637       CTT -> CTG
−
658 660 CTT -> CGG
+
658       CTT -> CGG
−
664 666 TCC -> TCT
+
664       TCC -> TCT
−
715 717 CTT -> CTG
+
711      A  -> C
−
754 756 GCC -> GCT
+
715       CTT -> CTG
−
763 765 CCA -> CCG
+
754       GCC -> GCT
−
766 768 CCT -> CCG
+
763       CCA -> CCG
−
772 774 CTC -> CTG
+
766       CCT -> CCG
−
775 777 AGA -> CGT
+
772       CTC -> CTG
−
784 786 CTT -> CTG
+
775       AGA -> CGT
−
787 789 GGG -> GGC
+
784       CTT -> CTG
−
805 807 CCT -> CCG
+
787       GGG -> GGC
−
829 831 GGG -> GGC
+
805       CCT -> CCG
−
838 840 CTT -> CTG
+
829       GGG -> GGC
−
862 864 ATA -> ATC
+
838       CTT -> CTG
 +
862       ATA -> ATC
  
 
===Source===
 
===Source===
  
−
https://www.ncbi.nlm.nih.gov/nuccore/AH003685, [https://parts.igem.org/Part:BBa_K5492400 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===

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.