Difference between revisions of "Part:BBa K1152014:Design"

 
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__NOTOC__
 
__NOTOC__
 
<partinfo>BBa_K1152014 short</partinfo>
 
<partinfo>BBa_K1152014 short</partinfo>
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===Design Notes===
 
===Design Notes===
−
x
+
The native indC contains an internal EcoRI and SpeI cutting site which was mutated using a CPEC approach. We amplified indC in three fragments from ''P. luminescens'' genomic DNA:
 +
# start codon to EcoRI cutting site (Primer 1/2; Table 1)
 +
# EcoRI cutting site to SpeI cutting site (Primer 3/4; Table 1)
 +
# Spe cutting site to stop codon (Primer 5/6; Table 1).<br/>
 +
The primers contain point mutation (indicated with small letters in Table 1) to remove the cutting sites. The backbone was amplified with the primers 7/8. Basically every backbone which contains the part [https://parts.igem.org/Part:BBa_K1152008 J04450] can be used.
 +
 
 +
{|class="wikitable"
 +
|+ Table 1: Primer for removal of internal RFC[10] cutting sites in indC using a CPEC approach
 +
|-
 +
!Name!!Primer Sequence 5' - 3'
 +
|-
 +
|1_indC_fw||CATACTAGAG AAAGAGGAGAAA GGTACC ATGTTAGAAAATAATATTACACAATG
 +
|-
 +
|2_EcoRI_rv||CAATACCCACC GAAcTC TTTGAGCT AATTTCTGACAGACAATACC
 +
|-
 +
|3_EcoRI_fw||AGCTCAAA GAgTTC GGTGGGTATTG GGCTTTTTTGTGATC
 +
|-
 +
|4_SpeI_rv||ATAAGCCAG ACTcGT GGGTTTAGGAACTTG GAACTTGAACTGTG
 +
|-
 +
|5_SpeI_fw||CAAGTTCCTAAACCC ACgAGT CTGGCTTAT ATTATTTATACCTCTGGTAGCAC
 +
|-
 +
|6_indC_rv||CAGCGTTATTA GCTAGC TCA TTAGATTATTTTCTCAATCTCAG
 +
|-
 +
|7_backbone_fw||TAATGA GCTAGC TAATAACGCTGATAGTGCTAGTG
 +
|-
 +
|8_backbone_rv||CAT GGTACC TTTCTCCTCTTT CTCTAGTATGTGTG
 +
|-
 +
|9_K1152013_fw|AAGTGGATTGAACAGACAGACTCTAAAAC
 +
|-
 +
|10_K1152013_rv|AGTATCTGTATGTAATGGCACCAATAGACGC
 +
|-
 +
|11_ccdB_fw|TGCCATTACATACAGATACT ACTGGCTGTGTATAAGGGAGCCTGAC
 +
|-
 +
|12_ccdB_rv|AGAGTCTGTCTGTTCAATCCACTT CGCGTGGATCCGGCTTAC
 +
|-
 +
|}
 +
 
 +
In a 6 ul PCR Master Mix (NEB Phusion High-Fidelity in High Fidelity buffer), all fragments were put together in an equimolar ratio. CPEC assembly was performed using an optimized protocol (Table 2).
 +
 
 +
{|class="wikitable"
 +
|+Table 2: CPEC assembly Cycler Parameters
 +
|-
 +
!Cycles!!Temperature [°C]!!Time [s]
 +
|-
 +
|1||98||30
 +
|-
 +
|rowspan="3"|5||98||5
 +
|-
 +
|53||15
 +
|-
 +
|72||60
 +
|-
 +
|1||72||180
 +
|-
 +
|}
 +
[[file:ccdB_TOP10.png|300px|thumb|right|''Figure 1'']]
 +
Transformation was performed with 5 ul of the CPEC reaction product.
 +
The resulting plasmid is [https://parts.igem.org/Part:BBa_K1152008 K1152008]. We subsequently amplified the plamid without the T-domain with primers 9/10 and the ccdB cassette from pDONR with primers 11/12. In a second CPEC assembly, the indC-ccdB part was created and transformed into OneShot ccdB survival cells.
 +
The prepped plasmid was then transformed into both ''E. coli'' TOP10 and OneShot cells, outlining that there are no background colonies (Figure 1).
  
  
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===Source===
 
===Source===
  
−
x
+
The coding sequence was amplified from ''Photorhabdus luminescens laumondii'' TT01 DSM15139.
  
 
===References===
 
===References===
 +
#Brachmann AO, Kirchner F, Kegler C, Kinski SC, Schmitt I, Bode HB (2012) Triggering the production of the cryptic blue pigment indigoidine from Photorhabdus luminescens. J Biotechnol 157: 96-99.
 +
#Quan J, Tian J (2009) Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One 4: e6441.

Revision as of 01:54, 6 October 2013

indC-ccdB


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 4572
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 1467
    Illegal BamHI site found at 3742
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 3192
    Illegal SapI.rc site found at 2730


Design Notes

The native indC contains an internal EcoRI and SpeI cutting site which was mutated using a CPEC approach. We amplified indC in three fragments from P. luminescens genomic DNA:

  1. start codon to EcoRI cutting site (Primer 1/2; Table 1)
  2. EcoRI cutting site to SpeI cutting site (Primer 3/4; Table 1)
  3. Spe cutting site to stop codon (Primer 5/6; Table 1).

The primers contain point mutation (indicated with small letters in Table 1) to remove the cutting sites. The backbone was amplified with the primers 7/8. Basically every backbone which contains the part J04450 can be used.

Table 1: Primer for removal of internal RFC[10] cutting sites in indC using a CPEC approach
Name Primer Sequence 5' - 3'
1_indC_fw CATACTAGAG AAAGAGGAGAAA GGTACC ATGTTAGAAAATAATATTACACAATG
2_EcoRI_rv CAATACCCACC GAAcTC TTTGAGCT AATTTCTGACAGACAATACC
3_EcoRI_fw AGCTCAAA GAgTTC GGTGGGTATTG GGCTTTTTTGTGATC
4_SpeI_rv ATAAGCCAG ACTcGT GGGTTTAGGAACTTG GAACTTGAACTGTG
5_SpeI_fw CAAGTTCCTAAACCC ACgAGT CTGGCTTAT ATTATTTATACCTCTGGTAGCAC
6_indC_rv CAGCGTTATTA GCTAGC TCA TTAGATTATTTTCTCAATCTCAG
7_backbone_fw TAATGA GCTAGC TAATAACGCTGATAGTGCTAGTG
8_backbone_rv CAT GGTACC TTTCTCCTCTTT CTCTAGTATGTGTG
AAGTGGATTGAACAGACAGACTCTAAAAC
AGTATCTGTATGTAATGGCACCAATAGACGC
TGCCATTACATACAGATACT ACTGGCTGTGTATAAGGGAGCCTGAC
AGAGTCTGTCTGTTCAATCCACTT CGCGTGGATCCGGCTTAC

In a 6 ul PCR Master Mix (NEB Phusion High-Fidelity in High Fidelity buffer), all fragments were put together in an equimolar ratio. CPEC assembly was performed using an optimized protocol (Table 2).

Table 2: CPEC assembly Cycler Parameters
Cycles Temperature [°C] Time [s]
1 98 30
5 98 5
53 15
72 60
1 72 180
Figure 1

Transformation was performed with 5 ul of the CPEC reaction product. The resulting plasmid is K1152008. We subsequently amplified the plamid without the T-domain with primers 9/10 and the ccdB cassette from pDONR with primers 11/12. In a second CPEC assembly, the indC-ccdB part was created and transformed into OneShot ccdB survival cells. The prepped plasmid was then transformed into both E. coli TOP10 and OneShot cells, outlining that there are no background colonies (Figure 1).


Source

The coding sequence was amplified from Photorhabdus luminescens laumondii TT01 DSM15139.

References

  1. Brachmann AO, Kirchner F, Kegler C, Kinski SC, Schmitt I, Bode HB (2012) Triggering the production of the cryptic blue pigment indigoidine from Photorhabdus luminescens. J Biotechnol 157: 96-99.
  2. Quan J, Tian J (2009) Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One 4: e6441.