Difference between revisions of "Part:BBa K3843002:Design"

(→‎Design Notes)
(→‎References)
Line 20: Line 20:
  
 
===References===
 
===References===
 +
Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C. & Ferrin, T. E. UCSF Chimera--a visualization system for exploratory research and analysis (Version 1.15). <i>J Comput Chem</i>. 2004; <i>25</i>(13): 1605-1612. https://www.ncbi.nlm.nih.gov/pubmed/15264254

Revision as of 18:09, 18 October 2021


1UTM-HRP (fusion)


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 1113
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 1077
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 1249


Design Notes

1UTM was translationally fused to horseradish peroxidase (HRP). Before use in the fusion, 1UTM's signal peptide was removed using the SignalP 5.0 server, and the last 142 bp were removed to produce the mature 1UTM polypeptide. HRP's signal peptide was removed using the SignalP 5.0 server, and introns were removed from the genomic DNA sequence to yield the properly functioning protein. A 6-His tag followed by a TEV protease linker was added at the N-terminus to allow for purification by Ni-NTA affinity chromatography. At the C-terminus, an Avi-tag was appended, allowing for biotinylation. A flexible, moderately long (13 AA), and polar linker (consisting of Ser and Thr) separated 1UTM and HRP, allowing for proper functioning and stability of the fusion protein in aqueous solution. The overall fusion protein sequence was codon optimized for E. coli K12, illegal restriction sites for RFC[25] were removed.

Source

The sequence of 1UTM was obtained from GenBank: https://www.ncbi.nlm.nih.gov/nuccore/X70071.

The genomic sequence of HRP was obtained from GenBank: https://www.ncbi.nlm.nih.gov/nuccore/M37156.

The sequence of the Ser-Thr linker was arbitrarily designed and obtained by back-translation of the desired amino acid sequence.

AVITAG? 6HIS+TEV?

References

Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C. & Ferrin, T. E. UCSF Chimera--a visualization system for exploratory research and analysis (Version 1.15). J Comput Chem. 2004; 25(13): 1605-1612. https://www.ncbi.nlm.nih.gov/pubmed/15264254