Team:NYMU-Taipei/notebook/labnotes

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       <h>Lab notes</h>
       <h>Lab notes</h>
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      <div id='tabframe'>
 
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        <div class='note-tab' id='nt1'>introduction</div>
 
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        <div class='note-tab' id='nt2'>control</div>
 
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        <div class='note-tab' id='nt3'>communication</div>
 
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        <div class='note-tab' id='nt4'>cohesion</div>
 
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        <div class='note-tab' id='nt5'>completion</div>
 
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        <div class='note-tab' id='nt6'>function test</div>
 
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      </div>
 
       <div id='labnote'>
       <div id='labnote'>
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         <div class='note-tab'>labnote 1</div>
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         <div class='note-content notenow' id='nt1-cont'>
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         <div class='note-tab'>labnote 2</div>
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<h1>introduction :P introduction :P introduction :P introduction :P </h1>
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         <div class='note-tab'>labnote 3</div>
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<p>introduction of labnote</p>
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         <div class='note-tab'>labnote 4</div>
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<p>樹狀圖 timeline 順序圖</p>
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<p>under construction</p>
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         <div class='note-content' id='nt2-cont' style='display:none;'>
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<h1>lab note of circuit in the control part</h1>
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<p>part/gene transformation and test</p>
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<p>circuit contruction</p>
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<p>part function test</p>
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<p>under construction</p>
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<h2>experiment1 date: 0707~0712</h2>
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<p>under construction</p>
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<p>under construction</p>
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<p>under construction</p>
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<p>under construction</p>
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<h2>experiment1 date: 0707~0712</h2>
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<p>under construction</p>
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<p>under construction</p>
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<p>under construction</p>
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<h2>experiment1 date: 0707~0712</h2>
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        </div>
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         <div class='note-content' id='nt3-cont' style='display:none;'>
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<h1>lab note of circuit in the communication part</h1>
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<p>part/gene transformation and test</p>
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<p>circuit contruction</p>
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<p>part function test</p>
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<p>under construction</p>
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<h2>experiment1 date: 0707~0712</h2>
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<p>under construction</p>
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<p>under construction</p>
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<h2>experiment1 date: 0707~0712</h2>
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<p>under construction</p>
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<p>under construction</p>
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<p>under construction</p>
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<h2>experiment1 date: 0707~0712</h2>
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<p>under construction</p>
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<p>under construction</p>
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        </div>
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        <div class='note-content' id='nt4-cont' style='display:none;'>
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<h1>lab note of circuit in the cohesion part</h1>
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<h2>Working Circuit Assembling</h2>
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<p><b>1. Check IGEM standard part-K523013(trunk).B0015</b></p>
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    <ol>
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      <li>IGEM kit transformation with DH5 competent cell</li>
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      <li>colony PCR check: pick up colony of transformation and do the PCR to check part length</li>
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      <li>plasmid PCR check: extract the plasmid of the correct length of part after checking colony PCR check, and use plasmid PCR to check length again</li>
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      <li>Digestion check: use enzyme to cut plasmid of correct length of PCR, to check restriction site</li>
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      <li>Second plate and liquid culture save: save bacteria containing correct plasmid in liquid culture and second plate</li>
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      <img src='/wiki/images/e/e8/NYMU14_note_3c_r1.PNG'>
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    </ol>
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<p><b>2. Get S. mutans competent signal peptide (CSP16) part</b></p>
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    <ol>
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      <li>S. mutans genome extraction </li>
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      <li>Tag PCR to get CSP16 linear DNA and check length through electrophoresis: we use Tag PCR to test the condition of the most suitable condition of PCR</li>
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      <li>KOD PCR to get CSP16 linear DNA, check length through electrophoresis, and gel extraction to get CSP16 part: in the condition tested during Tag PCR, we use designed primer and KOD PCR to amplify and copy CSP16 linear DNA , and run electrophoresis and gel extraction to get CSP16 part</li>
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      <li>Digestion check: use enzyme to cut plasmid of correct length of PCR, to check restriction site</li>
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      <li>Second plate and liquid culture save: save bacteria containing correct plasmid in liquid culture and second plate</li>
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    </ol>
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<p><b>3. K523013(trunk) and CSP16 assembling</b></p>
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    <ol>
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      <li>We use Tag PCR with designed primer to check suitable PCR condition</li>
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      <li>We conducted KOD PCR with designed primer to get K523013 assembled with CSP16 linear DNA and check length through electrophoresis, and gel extraction to get CSP16 plus K523013(trunk) part: in the condition tested during Tag PCR, we use designed primer and KOD PCR to assemble CSP16 linear DNA and K523013(trunk) , and run electrophoresis and gel extraction to get CSP16 assembled with K523013(trunk) part</li>
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      <img src='/wiki/images/1/13/NYMU14_note_3c_r2.PNG'>
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      <img src='/wiki/images/4/4d/NYMU14_note_3c_r3.PNG'>
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    </ol>
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<p><b>4. K523013 assembled with CSP16 and BBa-B0015 assembling</b></p>
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    <ol>
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      <li>K523013 assembled with CSP16 digestion: we use ECOR1 and SPET1 enzyme to digest K523013 assembledCSP16</li>
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      <li>BBa-B0015 digestion: we use ECOR1 and XBAL1 enzyme to digest BBa-B0015</li>
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      <li>K523013 assembled with CSP16and BBa-B0015 ligation: we use T4 ligase to ligase K523013 assembled with CSP16and BBa-B0015</li>
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      <li>transformation with DH5ɚ competent cell</li>
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      <li>After plasmid extraction of the ciucuit ,it ran PCR and electrophoresis to check length of circuit</li>
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      <li>digestion to check circuit length and restriction site </li>
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      <li>plasmid sequencing of the final circuit</li>
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      <img src='/wiki/images/5/58/NYMU14_note_3c_r4.PNG'>
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    </ol>
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<h2>Testing Circuit Assembling</h2>
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<p><b>1. Check IGEM standard part-E1010</b></p>
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    <ol>
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      <li>IGEM kit transformation with DH5ɚ competent cell</li>
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      <li>colony PCR check: pick up colony of transformation and do the PCR to check part length</li>
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      <li>plasmid PCR check: extract the plasmid of the correct length of part after checking colony PCR check, and use plasmid PCR to check length again</li>
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      <li>Digestion check: use enzyme to cut plasmid of correct length of PCR, to check restriction site</li>
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      <li>Second plate and liquid culture save: save bacteria containing correct plasmid in liquid culture and second plate</li>
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      <img src='/wiki/images/b/b0/NYMU14_note_3c_r5.PNG'>
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    </ol>
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<p><b>2. K523013 + CSP16 and E1010 assembling</b></p>
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    <ol>
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      <li>K523013 assembled with CSP16 digestion: we use ECOR1 and SPET1 enzyme to digest K523013 assembledCSP16</li>
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      <li>E1010 digestion: we use ECOR1 and XBAL1 enzyme to digest E1010</li>
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      <li>K523013 assembled with CSP16and E1010 ligation: we use T4 ligase to ligase K523013 assembled with CSP16and E1010</li>
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      <li>transformation with DH5 competent cell </li>
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      <li>plasmid extraction of the circuit and through PCR and electrophoresis to check length of circuit</li>
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      <li>digestion to check circuit length and restriction site of circuit</li>
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      <li>plasmid sequencing of the final circuit</li>
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      <img src='/wiki/images/5/51/NYMU14_note_3c_r6.PNG'>
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    </ol>
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<p><b>3. K523013 + CSP16 + E1010 and B0015 assembling</b></p>
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    <ol>
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      <li>K523013 assembled with CSP16 digestion: we use ECOR1 and SPET1 enzyme to digest K523013 assembledCSP16 and E1010</li>
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      <li>BBa-B0015 digestion: we use ECOR1 and XBAL1 enzyme to digest BBa-B0015</li>
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      <li>K523013 assembled with CSP16 assembled with E1010and BBa-B0015 ligation: we use T4 ligase to ligase K523013 assembled with CSP16 assembled with BBa-B0015</li>
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      <li>transformation with DH5 competent cell</li>
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      <li>plasmid extraction of the ciucuit and through PCR and electrophoresis to check length of circuit</li>
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      <li>digestion to check circuit length and restriction site of circuit</li>
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      <li>plasmid sequencing of the final circuit</li>
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      <img src='/wiki/images/a/a4/NYMU14_note_3c_r7.PNG'>
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      <img src='/wiki/images/d/d7/NYMU14_note_3c_r8.PNG'>
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    </ol>
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        </div>
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         <div class='note-content' id='nt5-cont' style='display:none;'>
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<h1>lab note of circuit in the completion part</h1>
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<h2>Parts from iGEM took kit</h2>
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<h3>Out line</h3>
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<p>For each part to be used in testing circuit:<br>BBa_J23100 , BBa_E1010, BBa_B0015</p>
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<img src=''><p>circuit 圖</p>
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<p>After transforming these plasmids into our competent cell, DH5a, we would take 3 steps to examine if we got the right product:</p>
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<ol>
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<li>Colony PCR and electrophoresis: Directly picking up colonies on designated antibiotic plate and do colony PCR with iGEM provided primers (VF2&VR), and then do electrophoresis to check the length of plasmid to confirm if the kit had been correctly transformed into E. coli.</li>
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<li>Plasmid PCR and electrophoresis: Colony PCR may not end up copying the right place, for there is extra DNA in the cell that is not the one of our interest. Therefore, we also check the length of the plasmid we which we transformed.</li>
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<li>Digestion and electrophoresis: After checking the length, we use EcoR1/Spe1 and Xba1/Pst1, and electrophoresis, to see if our constructed plasmid can be successfully digested.</li>
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</ol>
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<h3>Process</h3>
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<p>We encounter several difficulties during the process:</p>
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<ol>
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<li>In the transformation step, we couldn’t get transformation with the right PCR band at first. Even thought they do grow on the antibiotic plate, electrophoresis result doesn’t show any band. Therefore, we tried different ways trying to solve these problems.<br>First, we thought it was PCR problem, therefore, we tried colony PCR. However, it came out that it wasn’t the case.So we improve our transformation protocol. That is, after 1.5 hour of recovery in 37C incubator in 200ml LB, we centrifuge in 3.4 rpm for 20 seconds, and discard 150ml supernatant.<br>At the end, we result in putting concentrated transformed E.coli into our antibiotic plate. This way, we sequentially transformed several kits successfully.</li>
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<li>In the checking step, we’ve have contaminated electrophoresis result after colony PCR. That is, we got band in the negative well. To find out the ingredient causing contamination, we do several negative control changing different packing of ingredients. And find the contamination of our 10X DreamTaq Buffer.</li>
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</ol>
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<h3>Result</h3>
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<img src='/wiki/images/4/43/NYMU14_note_4c_r1.PNG' style='width:430px;'>
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<img src='/wiki/images/f/ff/NYMU14_note_4c_r2.PNG' style='width:430px;'>
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<img src='/wiki/images/a/a3/NYMU14_note_4c_r3.PNG' style='width:400px;'>
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<img src='/wiki/images/c/cd/NYMU14_note_4c_r4.PNG' style='width:450px;'>
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<img src='/wiki/images/e/eb/NYMU14_note_4c_r5.PNG' style='width:500px;'>
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<h2>Parts that needed extra PCR</hr>
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<h3>Outline</h3>
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<p>Two parts needed extra primer in order to get them:<br>yebF, RFP, and M102 orf19</p>
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<img src=''><p>circuit 圖</p>
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<p>And for each part, we do two kinds of PCR , one using Dream Tag, only to check the length to ensure we got our part.  And then we used KOD enzyme, together with magnesium cation, to check the length, furthermore, do gel extraction to get the part. That’s because KOD enzyme leads a more accurate PCR.</p>
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<ol>
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<li>For yebF, we designed primers to get the sequence we want yebF (its own ribosomal binding site included) from Escherichia coli MG1655.<br>Front Primer : <i>tttctagagGGAGAAAAACATGAAAAAAAGAGGGGCGTT</i>(with Xbal cutting site)<br>Reverse Primer : <i>attctgcagcggccgctactagtACGCCGCTGATATTCCGCCA</i>(with Spel and Pst1 cutting site)<br>The PCR product should be 389bp.</li>
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<li>Because the need of recombinant protein, the RFP downstream of yebF need to be specially designed in order to leave scar with multiple of 3. E1010 was used as template, and primers with specially designed cutting site is made:<br>Front Primer: <i>tttctagaGCTTCCTCCTCCGAAGACGTTATC</i><br>And normal iGEM reverse primer, VR</li>
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</ol>
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<h3>Process</h3>
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<p>While doing RFP PCR, we got extra band.<br>By adjusting PCR program, we finally got correct band.</p>
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<img src='/wiki/images/6/6b/NYMU14_note_4c_r6.PNG' style='width:450px;'>
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<h3>Result</h3>
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<img src='/wiki/images/1/12/NYMU14_note_4c_r7.PNG' style='width:450px;'>
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<img src='/wiki/images/f/fc/NYMU14_note_4c_r8.PNG' style='width:450px;'>
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<img src='/wiki/images/6/63/NYMU14_note_4c_r9.PNG' style='width:450px;'>
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<h2>Construction of the circuit</h2>
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<h3>Outline</h3>
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<p>Circuits needed to be constructed<br>J23119-(RBS)yebF-RFP-B0015<br>J23119_B0034_RFP-B0015<br>J23119-yebF-B0015<br>J23119-yebF-orf19-B0015<br>By repeatedly using back insert, we tried to achieve the final construction.We planned to constructed our first circuit by following steps:</p>
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<ol>
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<li>J23119(SP)+yebF(XP)</li>
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<li>J23119+yebF(SP)+RFP(XP)</li>
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<li>J23119+yebF+RFP(SP)+B0015(XP)</li>
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</ol>
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<h3>Process</h3>
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<p>During circuit construction, we encountered several problems:<br>First, we the enzyme that we own are from different companies. Our digestion enzyme Pst1 is from Fast Digestion, requiring FD buffer, while the Spel enzyme is from NEB, requiring the addition of NEB buffer 4 and BSA, or smart cut buffer.<br>
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Also, because that one of the part result from cutting is so small that it’s invisible in electrophoresis, we can only check if our product had been successfully cut by transformation. We also did electrophoresis, though, to check if the band would be good enough to do extraction. Finally, by doing checking transformation product after ligation, we can fully sure that we had the right digestion cut.<br>
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Our first ligation result shows that using FD buffer is absolutely impossible if we want to digest with Spel and Pst1. As shown on the graph, it might just stick back to the original plasmid.</p>
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<img src='/wiki/images/6/6f/NYMU14_note_4c_r10.PNG' style='width:450px;'>
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        </div>
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        <div class='note-content' id='nt6-cont' style='display:none;'>
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<h1>lab note of function test in phage</h1>
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<p>part/gene transformation and test</p>
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<p>circuit contruction</p>
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<p>part function test</p>
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<p>under construction</p>
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<h2>experiment1 date: 0707~0712</h2>
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<p>under construction</p>
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<p>under construction</p>
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<p>under construction</p>
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<p>under construction</p>
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<h2>experiment1 date: 0707~0712</h2>
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<p>under construction</p>
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<p>under construction</p>
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<p>under construction</p>
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<h2>experiment1 date: 0707~0712</h2>
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<p>under construction</p>
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<p>under construction</p>
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Revision as of 12:51, 16 October 2014

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