Coding

Part:BBa_K1298000:Design

Designed by: CoBRA Team   Group: iGEM14_CoBRA   (2014-06-10)

PcChia 1-1


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 519
    Illegal AgeI site found at 445
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI.rc site found at 3


Design Notes

While considering the design of the part, a change to the DNA sequence was required in order to avoid having the protein code cut at unwanted points (illegal cut sites) when doing a restriction digest. The DNA optimization was achieved. Also, in order to get the PcChia 1-1 code into a pSB1C3 backbone (required for submission to iGEM), the Red Fluorescent Protein (RFP) was removed from the part BBa_J04450 and the chitinase code was inserted. This was done in order to confirm that the E. coli bacteria being used had obtained the chitinase (red colonies would not have picked it up, whereas white ones did)

Source

Phytochemistry paper of Dr. Kolosova (1), NCBI (protein code) (2), Bio Basic Inc. (DNA optimization)

References

1. Kolosova, N. “Cloning and characterization of chitinases from interior spruce and lodgepole pine.” 1 Oct. 2013. Feb. 2014 <http://www.ncbi.nlm.nih.gov/pubmed/24564978>

2. Kolosova, N. "Pinus contorta class I chitinase (Chia1-1) mRNA, complete cds." 30 Dec. 2011. Feb. 2014 <http://www.ncbi.nlm.nih.gov/nuccore/HM219849> *

*The sequence found at this link has been optimized to remove illegal cut sites (EcoRI, XbaI, SpeI, PstI) and therefore is not the same as the sequence found on this part page.