Difference between revisions of "Part:BBa K1638035:Design"

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===Design Notes===
 
===Design Notes===
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A fragment of this part (linker_intein_scaffold) was synthesized by IDT as a gBlock gene fragment.
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A fragment of this part (linker_intein_scaffold) was synthesized by IDT as a gBlock gene fragment. This gene fragment was suffixed to the T18 domain of <i>cyaA</i> from <i>Bordetella pertussis</i> by digesting the two parts with BamHI and PstI followed by ligation.
  
  

Revision as of 09:44, 18 September 2015


hTrx-based scaffold fused to T18 through intein and a flexible linker


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 1563
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 1229
    Illegal BamHI site found at 711
    Illegal XhoI site found at 2374
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 252
    Illegal NgoMIV site found at 662
    Illegal NgoMIV site found at 2106
    Illegal AgeI site found at 468
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

A fragment of this part (linker_intein_scaffold) was synthesized by IDT as a gBlock gene fragment. This gene fragment was suffixed to the T18 domain of cyaA from Bordetella pertussis by digesting the two parts with BamHI and PstI followed by ligation.


Library

  • Choose the size of your library. Typically the length of the variable peptide loop is between 10 and 20 amino acids.
  • Dependent on the size your variable peptide loop, you can for example contruct the library as following: ATATGCGCTCGAG(NNK)xGAGCTCATTACCG (where N represent A, T, G or C and K represent G or C). The NNK codon minimizes the number of stop codons. The XhoI restriction included allows insertion of library into the scaffold.
  • Order the library as duplex-DNA
  • When delivered, cut the library and scaffold with XhoI restriction enzyme and ligate.

Important note: This part cannot be used in the standard backbones pSB1C3 or pSB1K3, as they include a xhoI restriction site. Instead we recommend using the pSB1A2 backbone

Source

..

References