Team:UIUC-Illinois/Notebook

From 2011.igem.org

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         <div class="desc"><img src="https://static.igem.org/mediawiki/2011/6/6a/Uiuc_notebook_2.jpg" /></div>
         <div class="desc"><img src="https://static.igem.org/mediawiki/2011/6/6a/Uiuc_notebook_2.jpg" /></div>
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        <div class="desc">Primers:</div>
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        <div class="desc">ATCG  <font color="red">T ACTAGT A GCGGCCG CTGCAG</font> CAGTGAATTAATGGCGATGACGC</div>
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        <div class="desc">Tm = 68 C</div>
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        <div class="desc">GC = 48%</div>
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        <div class="desc">ATCG ACTAGTA <font color="green">CTCTAGAAGCGGCCGCGAATTC</font>  GCATGCAAGCTTGGCACTGG</div>
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        <div class="desc">Tm = 64 C</div>
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        <div class="desc">GC = 60%</div>
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        <br><br>
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        <div class="desc">The following PCR rxn was then set up and run with the subsequent parameters:</div>
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        <div class="desc">0.3 uL pAH125</div>
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        <div class="desc">2uL primer 1 (100ng/uL)</div>
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        <div class="desc">2uL primer2 (100ng/uL)</div>
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        <div class="desc">5uL 10X Pfu buffer (Agilent)</div>
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        <div class="desc">2.5uL 10mM dNTP mix</div>
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        <div class="desc">1uL Turbo Polymerase (Agilent)</div>
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        <div class="desc">37uL ddH2O</div>
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        <br><br>
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        <div class="desc">95C 5 min</div>
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        <div class="desc">95C 30sec</div>
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        <div class="desc">59C 30 sec</div>
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        <div class="desc">72C 3 min</div>
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        <div class="desc">Cycle 30X</div>
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        <div class="desc">72C 5 min</div>
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        <div class="desc">14C forever</div>
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        <br><br>
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        <div class="desc">The pcr rxn was then  purified using a Qiagen pcr purification kit.  Resulting concentration was 99ng/uL.</div>
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        <div class="desc">500ng of the reaction was then digested SpeI with the following reaction set up:</div>
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        <div class="desc">0.5uL pcr product</div>
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        <div class="desc">5uL NEB Buffer 2</div>
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        <div class="desc">1uL 100X BSA</div>
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        <div class="desc">1uL SpeI (from NEB)</div>
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        <div class="desc">42.5uL ddH2O</div>
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        <br><br>
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        <div class="desc">Digest ran 1 hour 37C and was followed by an 80C heat inactivation.</div>
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        <br><br>
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        <div class="desc">2uL of the digestion reaction was then used in a 20 uL volume ligation reaction.  Set up was as follows:</div>
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        <div class="desc">2uL SpeI digest</div>
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        <div class="desc">2uL 10X Promega T4 ligase buffer</div>
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        <div class="desc">1uL Promega T4 ligase</div>
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        <div class="desc">15uL ddH2O</div>
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        <br><br>
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        <div class="desc">Ligation reaction ran at for 8 hours at 15C.</div>
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        <br><br>
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        <div class="desc">3uL of the ligation reaction was then transformed into two strains via heat shock as described in our protocol download.  The first strain was a normal pir- DH5alpha E. coli strain and the second was a E. coli K-12 pir-116 strain.  The latter should allow replication of the plasmid while the first should not.  The transformations were plated on LB kan 30ug/mL.  Plates were incubated 18 hours at 37C.  The following pictures show that robust colonies resulted on the pir-116 transformant plate but not on the pir- DH5alpha plate.</div>
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Revision as of 03:35, 29 September 2011

University of Illinois iGEM Team
About the Team
Team Navigation
Notebook
OpenWetWare Notebook

Who We Are
Amanda Chang
"A watched gel never runs"
Plasmid Integration Protocol (for CRIM plasmids)
1. Prepare electrocompetent cells that have been transformed with the helper plasmid (pAH57) and that have been grown in 5 mL SOB to an OD of 600nm of ca. 0.6 with ampicillin antibiotic at 30 degC.
2. Perform an electroporation transformation with the BioBrick Compatible Lambda Chromosomal Insertion Plasmid making sure to resuspend the cells in 1 mL of SOC (without ampicillin). Incubate at 37 degC for 1 hour, and then 42 degC for 30 minutes. Spread plate onto a selective agar plate and incubate at 37 degC.
K617000 Creation
Day 1
The CRIM pAH125 vector was obtained in a pir+ strain. The culture was streaked from the -80C onto a LB kanamycin 30ug/mL plate. Plate was incubated 37C for 18 hours. White colonies resulted.
A single colony was picked from the previous plate and was used to inoculate 6mL of LB kanamycin 30ug/mL. The culture was then incubated 37C on a tube turner for 16 hours. A turbid yellow-white culture resulted.
5mL of the culture was pelleted and miniprepped using the Promega mini-prep kit and protocol described in our protocol download. The resulting concentration was 30ng/uL.
The plasmid map of pAH125 is shown below:
The following primers were then designed in order to amplify the highlighted (red)section below. The primers contain overhangs such that subsequent SpeI digestion and an intramolecular ligation of the pcr product will produce a biobrick cloning site, which replaces the original MCS and lacZ ORF in the pAH125 diagram.
Primers:
ATCG T ACTAGT A GCGGCCG CTGCAG CAGTGAATTAATGGCGATGACGC
Tm = 68 C
GC = 48%
ATCG ACTAGTA CTCTAGAAGCGGCCGCGAATTC GCATGCAAGCTTGGCACTGG
Tm = 64 C
GC = 60%


The following PCR rxn was then set up and run with the subsequent parameters:
0.3 uL pAH125
2uL primer 1 (100ng/uL)
2uL primer2 (100ng/uL)
5uL 10X Pfu buffer (Agilent)
2.5uL 10mM dNTP mix
1uL Turbo Polymerase (Agilent)
37uL ddH2O


95C 5 min
95C 30sec
59C 30 sec
72C 3 min
Cycle 30X
72C 5 min
14C forever


The pcr rxn was then purified using a Qiagen pcr purification kit. Resulting concentration was 99ng/uL.
500ng of the reaction was then digested SpeI with the following reaction set up:
0.5uL pcr product
5uL NEB Buffer 2
1uL 100X BSA
1uL SpeI (from NEB)
42.5uL ddH2O


Digest ran 1 hour 37C and was followed by an 80C heat inactivation.


2uL of the digestion reaction was then used in a 20 uL volume ligation reaction. Set up was as follows:


2uL SpeI digest
2uL 10X Promega T4 ligase buffer
1uL Promega T4 ligase
15uL ddH2O


Ligation reaction ran at for 8 hours at 15C.


3uL of the ligation reaction was then transformed into two strains via heat shock as described in our protocol download. The first strain was a normal pir- DH5alpha E. coli strain and the second was a E. coli K-12 pir-116 strain. The latter should allow replication of the plasmid while the first should not. The transformations were plated on LB kan 30ug/mL. Plates were incubated 18 hours at 37C. The following pictures show that robust colonies resulted on the pir-116 transformant plate but not on the pir- DH5alpha plate.


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