Difference between revisions of "Part:BBa K1431302:Design"
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<center>'''Fig.2  PCR Product Sequence'''</center>
 
<center>'''Fig.2  PCR Product Sequence'''</center>
  
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And the reason why we designed that because we want to make a seamless gather between NLS and protein or any triple nucleotides. That depend on which will make the highest efficiency.
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And the reason why we designed that because we want to make a seamless gather between promoter and protein or any number nucleotides. That depend on which will make the highest efficiency.
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===Protocol===
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#Design the primers show below:<br>SV40 promoter forward: T TCTAGA G CGAACTGTGGAATGTGTG<br>SV40 promoter reverse: ACGCA GGATCC AT GAAGAC GACGAAAATGGATATACAAG<br>SV40 PolyA forward: ACGCG AGATCT AT GAAGAC CCAACTTGTTTATTGCAGCTTA<br>SV40 PolyA reverse: AAAACTGCAG CGGCCGC T ACTAGT A TCCATGCCGAGAGTGATGAA
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#Dissolve the primers into 50pmol/μl
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#PCR SV40 promoter and SV40 PolyA by the protocol below:<br> https://static.igem.org/mediawiki/parts/7/7f/2014_SUSTC-Shenzhen_taq_PCR_protocol.png<br>'''Thermocycling Conditions for a Routine PCR:'''<br>https://static.igem.org/mediawiki/parts/d/d2/SUSTC_Thermocycling_Conditions_for_a_Routine_PCR.png
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#By Gel Purification Kit, purify SV40 promoter and SV40 PolyA
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#Using Nanodrop to get each sample’s concentration
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#Digest SV40 by XbaI and BamHI, SV40 PolyA by BglII and PstI overnight. The digest protocol shows below:<br>https://static.igem.org/mediawiki/parts/e/ec/SUSTC_digest_system.png
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#Purify SV40 promoter and SV40 PolyA again
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#Ligase vector, promoter and PolyA at 16℃ for 45min and inactive at 60℃ for 10min. Ligation protocol shows:<br>https://static.igem.org/mediawiki/parts/2/26/SUSTC_ligase.png
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#Transfect the plasmid into DH5α supercompetent cells
  
 
===Sequencing Results===
 
===Sequencing Results===

Revision as of 21:01, 26 October 2014

SV40 promoter+SV40 PolyA


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

For BbsI site, we have a series same design sequence. See the mechanism of BbsI site work below.

20141018014544%21Our_RFC.png
Fig.1 The Machanism of Our Standard

If you want to insert a coding sequence between promoter and polyA, the prefix of forward primer you design must contain GAAGACNNtaaaNNNN and reverse must contain GAAGACNNagttNNNN. The middle two Ns would be any bases for them will be cut off and the four Ns should be begins or ends of the coding sequence. You can get parts by above primers and digest by BbsI restriction enzyme. Then you can insert the parts into promoter and polyA seamless. The PCR product must be such sequence, including the protect bases, shows below.

PCR_product_by_new_RFC.png
Fig.2 PCR Product Sequence

And the reason why we designed that because we want to make a seamless gather between promoter and protein or any number nucleotides. That depend on which will make the highest efficiency.

Protocol

  1. Design the primers show below:
    SV40 promoter forward: T TCTAGA G CGAACTGTGGAATGTGTG
    SV40 promoter reverse: ACGCA GGATCC AT GAAGAC GACGAAAATGGATATACAAG
    SV40 PolyA forward: ACGCG AGATCT AT GAAGAC CCAACTTGTTTATTGCAGCTTA
    SV40 PolyA reverse: AAAACTGCAG CGGCCGC T ACTAGT A TCCATGCCGAGAGTGATGAA
  2. Dissolve the primers into 50pmol/μl
  3. PCR SV40 promoter and SV40 PolyA by the protocol below:
    2014_SUSTC-Shenzhen_taq_PCR_protocol.png
    Thermocycling Conditions for a Routine PCR:
    SUSTC_Thermocycling_Conditions_for_a_Routine_PCR.png
  4. By Gel Purification Kit, purify SV40 promoter and SV40 PolyA
  5. Using Nanodrop to get each sample’s concentration
  6. Digest SV40 by XbaI and BamHI, SV40 PolyA by BglII and PstI overnight. The digest protocol shows below:
    SUSTC_digest_system.png
  7. Purify SV40 promoter and SV40 PolyA again
  8. Ligase vector, promoter and PolyA at 16℃ for 45min and inactive at 60℃ for 10min. Ligation protocol shows:
    SUSTC_ligase.png
  9. Transfect the plasmid into DH5α supercompetent cells

Sequencing Results

We sent fresh bacteria broth for sequencing using standard Biobricks sequencing primer VF2/VR. The sequencing cooperation we used is Invitrogen Guangzhou filiale.

Sequence of sequencing primer we used:
VF2: tgccacctgacgtctaagaa
VR: attaccgcctttgagtgagc

The result shows the same sequence with our ideal design.

Source

The plasmid was from our instructor, Huangwei's lab. And we design primers to copy down by PCR.