Difference between revisions of "Part:BBa K1298002:Design"

 
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<partinfo>BBa_K1298002 short</partinfo>
 
<partinfo>BBa_K1298002 short</partinfo>
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===Design Notes===
 
===Design Notes===
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Avoiding illegal cutsites.
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While considering the design of the part, a modification to the DNA sequence of the chitinase was required in order to avoid cutting the protein code cut at unwanted sites (illegal cut sites) during a restriction digest. The DNA optimization was successful. It should also be noted that the PgeChia 1-2 was put into a pSB1C3 backbone, the BBa_J04450 part was used. The Red Fluorescent Protein (RFP) was replaced with the chitinase in order to check that the E. coli bacteria being used had obtained the protein code for chitinase (Red colonies had not had the RFP replaced, but the white ones would have)
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+
  
  
 
===Source===
 
===Source===
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Phytochemistry paper of Dr. Kolosova (1), NCBI (protein code) (2), Bio Basic Inc. (DNA optimization)
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BioBasic Optimized DNA
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===References===
 
===References===
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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>
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2. Kolosova, N. "Picea engelmannii x Picea glauca class I chitinase (Chia1-1) mRNA, complete cds." 30 Dec. 2013. Feb. 2014 <http://www.ncbi.nlm.nih.gov/nuccore/HM219844> *
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<p> *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.

Revision as of 22:51, 17 June 2014

PgeChia1-2


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 586
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 496
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 567
    Illegal BsaI site found at 818


Design Notes

While considering the design of the part, a modification to the DNA sequence of the chitinase was required in order to avoid cutting the protein code cut at unwanted sites (illegal cut sites) during a restriction digest. The DNA optimization was successful. It should also be noted that the PgeChia 1-2 was put into a pSB1C3 backbone, the BBa_J04450 part was used. The Red Fluorescent Protein (RFP) was replaced with the chitinase in order to check that the E. coli bacteria being used had obtained the protein code for chitinase (Red colonies had not had the RFP replaced, but the white ones would have)


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. "Picea engelmannii x Picea glauca class I chitinase (Chia1-1) mRNA, complete cds." 30 Dec. 2013. Feb. 2014 <http://www.ncbi.nlm.nih.gov/nuccore/HM219844> *

*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.