Difference between revisions of "Part:BBa K1951002:Design"

 
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===Sequence optimization===
  
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__NOTOC__
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Snapgene has been used to remove the forbidden sites by changing in the substitution which didn't change the amino acid. The sequence has been sythetised by IDT<ref>http://eu.idtdna.com/site</ref>.
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<partinfo>BBa_K1951002 short</partinfo>
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<partinfo>BBa_K1951002 SequenceAndFeatures</partinfo>
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===Codon optimization for <i>Escherichia coli</i>. ===
  
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We obtimised codon for <i>Escherichia coli</i>. Codon optimization is a technical used to <u>improve the protein expression</u> in living organism by increasing the translational efficiency of gene of interest [1-4, 6-13, 15-18, 20-28]. This biobrick codon optimised <u>increase the functionality of gene</u>. To process it, we use codon optimization IDT software<ref> https://eu.idtdna.com/CodonOpt </ref>.
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If you use this biobrick in <i>Escherichia coli</i>, you can be sure that the protein produced will be highly expressed and well solubilised.
  
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===Design Notes===
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=== Prefix and suffix addition===
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We added prefix and suffix sequences containing the restriction sites (EcoR1, XbaI and SpeI, PstI respectively)
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Prefix and suffix subsequences (containing restriction site EcoRI, XbaI and SpeI PstI respectively) have been added by a SLIC method with the following oligos :
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{| class="wikitable"
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| desC slic forward 
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| cgctaaggatgatttctgGAATTCGCGGCCGCTTCTAGATGTCTCGCCTTTCCACG
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|-
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| desC slic reverse
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| ttgcccttttttgccggaCTGCAGCGGCCGCTACTAGTATTATTAGGCTGAAACCGC
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|}.
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===Sequence and features===
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<partinfo>BBa_K1951002 SequenceAndFeatures</partinfo>
  
  

Revision as of 13:37, 17 October 2016

Sequence optimization

Snapgene has been used to remove the forbidden sites by changing in the substitution which didn't change the amino acid. The sequence has been sythetised by IDT[1].

Codon optimization for Escherichia coli.

We obtimised codon for Escherichia coli. Codon optimization is a technical used to improve the protein expression in living organism by increasing the translational efficiency of gene of interest [1-4, 6-13, 15-18, 20-28]. This biobrick codon optimised increase the functionality of gene. To process it, we use codon optimization IDT software[2]. If you use this biobrick in Escherichia coli, you can be sure that the protein produced will be highly expressed and well solubilised.

Prefix and suffix addition

Prefix and suffix subsequences (containing restriction site EcoRI, XbaI and SpeI PstI respectively) have been added by a SLIC method with the following oligos :

desC slic forward cgctaaggatgatttctgGAATTCGCGGCCGCTTCTAGATGTCTCGCCTTTCCACG
desC slic reverse ttgcccttttttgccggaCTGCAGCGGCCGCTACTAGTATTATTAGGCTGAAACCGC
.

Sequence and features


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]


Source

The following website gave us information about the gene reference and his chromosomal location. http://strepdb.streptomyces.org.uk/cgi-bin/dc3.pl?accession=AL645882&serial=2769&width=900&start=3031362&end=3041362&iorm=map Start : 3038344 End : 3038898 The coding sequence ised comes from the website below :

http://www.ncbi.nlm.nih.gov/nuccore/NC_003888.3


References

  1. ↑ http://eu.idtdna.com/site
  2. ↑ https://eu.idtdna.com/CodonOpt