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

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

Revision as of 09:05, 15 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 in the following positions:

Start End note 10 12 TCC -> TCT 16 18 AGG -> CGT 58 60 CGG -> CGT 61 63 AGG-> CGT 67 69 CTC -> CTG 76 78 TCC -> TCT 121 123 CCA -> CCG 127 129 ATA -> ATC 130 132 ATA -> ATC 136 138 AGG -> CGT 175 177 ATA -> ATC 202 204 CTT -> CTG 211 213 CTC -> CTG 214 216 TCC -> TCT 235 237 CCA -> CCG 268 270 CCA -> CCG 286 288 GCC -> GCT 301 303 CTT -> CTG 307 309 GCC -> GCT 322 324 CTC -> CTG 376 378 AGA -> CGT 397 399 CTT -> CTG 454 456 CCA -> CCG 481 483 CTC -> CTG 484 486 TTA - > CTG 505 507 CTC -> CTG 571 573 CCC -> CCG 583 585 CTC -> CTG 610 612 CTC -> CTG 634 636 GGG -> GGC 637 639 CTT -> CTG 658 660 CTT -> CGG 664 666 TCC -> TCT 715 717 CTT -> CTG 754 756 GCC -> GCT 763 765 CCA -> CCG 766 768 CCT -> CCG 772 774 CTC -> CTG 775 777 AGA -> CGT 784 786 CTT -> CTG 787 789 GGG -> GGC 805 807 CCT -> CCG 829 831 GGG -> GGC 838 840 CTT -> CTG 862 864 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.