Difference between revisions of "Part:BBa K192000:Design"
 
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===Design Notes===
 
===Design Notes===
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Sequence was PCR'd from T. Maritima.  An additional tga stop site was added.
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Sequence was PCR'd from ''T. Maritima''.  An additional TGA stop site was added.
  
  
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**5'CTT CTA GAT GGA ATT TCT GAA AAG ATC
 
**5'CTT CTA GAT GGA ATT TCT GAA AAG ATC
  
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**Backward Primer  
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*Backward Primer  
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*** 5'CTA CTA GTA TCA TCA GAA CTT TAG AAG AAT CA
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** 5'CTA CTA GTA TCA TCA GAA CTT TAG AAG AAT CA
  
 
*TD-PCR amplification temperatures:
 
*TD-PCR amplification temperatures:
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===Source===
 
===Source===
  
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Thermotoga Maritima
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''Thermotoga Maritima''
  
 
===References===
 
===References===
 +
 +
Structural basis of enzyme encapsulation into a bacterial nanocompartment.
 +
Sutter M, Boehringer D, Gutmann S, Günther S, Prangishvili D, Loessner MJ, Stetter KO, Weber-Ban E, Ban N.
 +
Nat Struct Mol Biol. 2008 Sep;15(9):939-47.
 +
 +
PMID: 19172747

Latest revision as of 22:56, 21 October 2009

Encapsulin


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 74
    Illegal XhoI site found at 274
    Illegal XhoI site found at 568
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Sequence was PCR'd from T. Maritima. An additional TGA stop site was added.


Helpful Tips

TD-PCR

  • Forward Primer
    • 5'CTT CTA GAT GGA ATT TCT GAA AAG ATC
  • Backward Primer
    • 5'CTA CTA GTA TCA TCA GAA CTT TAG AAG AAT CA
  • TD-PCR amplification temperatures:

Notes

  • Primers
    • The primers used and noted above contain a SpeI site downstream and a Xbal site upstream for "easy" ligation into a biobrick plasmid.
  • Polymerase that was used was KapaHiFi (Engineered variant of of Taq)
    • Required to increase the [] of MgCl2.
    • After amplification at the specified TD-PCR program there was no unexpected bands


Suggestions

  • Primers
    • For better enzymatic digestion of SpeI and Xbal it was suggested to extend the primers beyond the recognition sequence by a few base pairs to allow something for the enzymes get a "grip-on"
      • As long as 3' end of primer is complementary there should be no issues with primer annealing.
    • TD-PCR was done to ensure we had product to extract and subject to another round of PCR to optimize , however due to lack of non-specific products the PCR protocol was never optimized.

Source

Thermotoga Maritima

References

Structural basis of enzyme encapsulation into a bacterial nanocompartment. Sutter M, Boehringer D, Gutmann S, Günther S, Prangishvili D, Loessner MJ, Stetter KO, Weber-Ban E, Ban N. Nat Struct Mol Biol. 2008 Sep;15(9):939-47.

PMID: 19172747