Difference between revisions of "Part:BBa K3140006:Design"

 
Line 7: Line 7:
  
 
===Design Notes===
 
===Design Notes===
−
N/A
 
  
 +
This part was based on the native VVD protein from (''Neurospora crassa''). The VVD36 coding sequence was generated by removing the first 36 amino acid residues and appending a start codon to the start of this truncated sequence. The cystine residue at position 73 (TGC) was then changed to alanine by changing the codon to GCC to yield VVD36-C73A. This sequence was then run through the Codonator 3000, with ''E. coli'' set as the destination organism. The output sequence from the rank order harmonisation method was then used as the final coding sequence in this part, VVD36-C73A-CH1.
  
 +
This part was intended for use in pK18 as a test of our codon harmonisation model. To achieve this, the part was ordered in a gBlock flanked by EcoRI and HindIII sites to enable traditional restriction cloning into pK18. A RBS sequence was added to the gBlock upstream of the part. The RBS sequence used was the consensus Shine-Dalgarno sequence.
  
 
===Source===
 
===Source===
  
−
N. crassa
+
The native sequence for VVD (''Neurospora crassa'') was obtained from NCBI (GenBank accession [https://www.ncbi.nlm.nih.gov/nuccore/AF338412.1 AF338412.1]).
  
 
===References===
 
===References===
 +
'''1.''' Schwerdtfeger, C. & Linden, H. VIVID is a flavoprotein and serves as a fungal blue light photoreceptor for photoadaptation. ''EMBO J'' '''22''', 4846-55 (2003).
 +
'''2.''' Zoltowski, B.D. ''et al.'' Conformational switching in the fungal light sensor Vivid. ''Science'' '''316''', 1054-7 (2007).

Revision as of 10:56, 21 October 2019


VVD36-C73A-CH1 (rank order harmonised)


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

This part was based on the native VVD protein from (Neurospora crassa). The VVD36 coding sequence was generated by removing the first 36 amino acid residues and appending a start codon to the start of this truncated sequence. The cystine residue at position 73 (TGC) was then changed to alanine by changing the codon to GCC to yield VVD36-C73A. This sequence was then run through the Codonator 3000, with E. coli set as the destination organism. The output sequence from the rank order harmonisation method was then used as the final coding sequence in this part, VVD36-C73A-CH1.

This part was intended for use in pK18 as a test of our codon harmonisation model. To achieve this, the part was ordered in a gBlock flanked by EcoRI and HindIII sites to enable traditional restriction cloning into pK18. A RBS sequence was added to the gBlock upstream of the part. The RBS sequence used was the consensus Shine-Dalgarno sequence.

Source

The native sequence for VVD (Neurospora crassa) was obtained from NCBI (GenBank accession AF338412.1).

References

1. Schwerdtfeger, C. & Linden, H. VIVID is a flavoprotein and serves as a fungal blue light photoreceptor for photoadaptation. EMBO J 22, 4846-55 (2003). 2. Zoltowski, B.D. et al. Conformational switching in the fungal light sensor Vivid. Science 316, 1054-7 (2007).