IGEM:Imperial/2010/Vectors team: Difference between revisions
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====Week 7==== | ====Week 7==== | ||
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<table width="1000px" border="0"> | |||
<tr> | |||
<td style="background-color:#FFFF66"> | |||
<b>Week 7</b> | |||
</td> | |||
<td style="background-color:#33ffff;"><b>Monday</b> | |||
</td> | |||
<td style="background-color:#33ffff;"><b>Tuesday</b> | |||
</td> | |||
<td style="background-color:#33ffff;"><b>Wednesday</b> | |||
</td> | |||
<td style="background-color:#33ffff;"><b>Thursday</b> | |||
</td> | |||
<td style="background-color:#33ffff;"><b>Friday</b> | |||
</td> | |||
</tr> | |||
<tr> | |||
<td style="background-color:#FF6666;width:100px;text-align:top;"><b>Morning</b> | |||
</td> | |||
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>Restriction digestion of 5' ins [K143008] (using Eco and Spe)</li> | |||
<li>PCR amplification of vector backbone pSB1C3</li> | |||
</ul> | |||
</td> | |||
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>Gel analysis and extraction of 5' ins</li> | |||
<li>Gel purification of 5' ins</li> | |||
<li>Restriction digestion of pSB1C3 (using Eco and Pst)</li> | |||
<li>PCR purification of pSB1C3 after digestion</li> | |||
<li>Gel analysis of 5' ins, dif and pSB1C3 to work out ratios for ligation</li> | |||
< | <li>Restriction digestion of pveg promoter and RBS [K143053] (using Eco and Spe)</li> | ||
< | <li>Restriction digetion of SpecR-T [K143065] (using Xba and Pst)</li> | ||
</ul> | |||
< | |||
</ | |||
</td> | |||
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>Replica plating and colony PCR of transformed colonies (containing 5' dif in pSB1C3)</li> | |||
<li>Gel extraction and PCR purification of pveg and SpecR-T in preparation for ligations this afternoon</li> | |||
<li>Gel analysis of pveg , Spec-T and pSB1C3 in order to work out ratios for the ligation</li> | |||
</ul> | |||
</td> | |||
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>Transformation of overnight ligations: 5' ins, dif with pSB1C3 and pveg, SpecR-T and pSB1C3 </li> | |||
</ul> | |||
</td> | |||
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>Replica plating and colony PCR of: 5' ins, dif with pSB1C3 and pveg, SpecR-T and pSB1C3 </li> | |||
</ul> | |||
</td> | |||
</tr> | |||
<tr> | |||
<td style="background-color:#ff6666;width:100px;text-align:top;"><b>Afternoon</b> | |||
</td> | |||
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>PCR purification of PSB1C3 vector </li> | |||
</ul> | |||
</td> | |||
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>Ligation of 5' ins and dif with pSB1C3 - a bench ligation (1 hour) and an overnight ligation were set up </li> | |||
<li>Transformation of E.Coli with the bench ligated products</li> | |||
<li>Gel analysis and extraction of pveg and SpecR-T</li> | |||
</ul> | |||
</td> | |||
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>Overnight ligation of pveg and SpecR-T with pSB1C3 </li> | |||
</ul> | |||
</td> | |||
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> | |||
</td> | |||
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>Gel analysis of colony PCR products from the transformations</li> | |||
<li> Overnight annealing of diff PES (Synthesized oligo)</li> | |||
</ul> | |||
</td> | |||
</tr> | |||
</table> | |||
</html> | |||
=====Monday, August 16===== | =====Monday, August 16===== |
Revision as of 09:33, 8 September 2010
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <title>Imperial iGEM 2010</title> <script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"></script> <script type="text/javascript"> $(document).ready(function(){ $("ul[id|=poplist]").hide();
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<p id="popshow">Follow our progress: Click me!</p> <div id="popcon"> <ul id="poplist"> <li><a href="#Objectives" class="popt">Objectives</a></li> <li><a href="#Assembly_of_Vectors" class="popt">Assembly of Vectors</a></li> <li><a href="#Schedule" class="popt">Schedule</a></li> <li><a href="#Lab_Notes" class="popt">Lab Notes</a></li>
</ul>
</div>
</body> </html>
Objectives
We are assembling the AmyE and PyrD vectors in order to transform B. Subtilis with our parts. Once completed, these vectors will be reusable and can then be used to introduce any relevant piece of DNA directly into B.subtilis genome. The vectors will be used both for the final assembly and for testing constructs.
- Assemble the PyrD vector
- Assemble the AmyE vector
Assembly of Vectors
Starting from the top, we are assembling the first two fragments (K14070 and K14064) and K147002 with our oligos to add in a Dif site. Two dif sites on either side of resistance cassettes can be used to later excise antibiotic resistance from our final constructs.
- K14070 and K14064 fragments
- DNA was taken out of the reigstry - Cut with restriction enzymes - Run on a gel to confirm correct cutting and estimate relative ratios of DNA for ligation - Ligated overnight - Transformed into E.Coli to Amplify the DNA - Colony PCR has been used to confirm the correct insert size.
- Next Steps:
- Extract the DNA with a miniprep - Proceed to the next step - Reverse PCR
- K14002 and oligos
- Ligated two single stranded oligos together to produce Dif and insertion site - Standard biobrick assembly of oligos to K14002 - Ligation and transformation into E.coli competent cells (strain) - Screen plated colonies for correct insertion
- Next Steps
- Purify the correct insert out of E.coli - Next step assembly - LacI test vector and Final assembly vector
- LacI Testing vector
- Currently waiting for Part B step 2 Midi-prep results to start this step
Schedule & Lab notes
PyrD Vector
Week 6
<html> <table width="1000px" border="0">
<tr> <td style="background-color:#FFFF66"> <b>Week 6</b> </td>
<td style="background-color:#33ffff;"><b>Monday</b>
</td> <td style="background-color:#33ffff;"><b>Tuesday</b> </td> <td style="background-color:#33ffff;"><b>Wednesday</b> </td> <td style="background-color:#33ffff;"><b>Thursday</b> </td> <td style="background-color:#33ffff;"><b>Friday</b> </td> </tr> <tr> <td style="background-color:#FF6666;width:100px;text-align:top;"><b>Morning</b> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> <ul> <li>Restriction digestion of 5' dif XP ( Using XbaI and PstI) </li> </ul> </td> </tr>
<tr>
<td style="background-color:#ff6666;width:100px;text-align:top;"><b>Afternoon</b>
</td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> <ul> <li>Start assembly of PyrD vector</li> <li>Overnight annealing of 5' Ins ( synthesized oligos )</li> </ul> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> <ul> <li>Gel analysis of resultant products from 5' dif XP digestion</li> <li.>PCR purification of 5' dif XP</li> <li></li> </ul> </td> </tr> </table> </html>
Thursday, August 12
- Annealing the forward and reverse strands of the dif XP oligo
The forward and reverse strands of the 5' dif site with XbaI and PstI restriction sites on either side have been synthesized separately. The synthesized fragments arrive in solid powder form. These were immediately diluted in ddH2O to obtain a stock concentration of 1 ng/ul. They were then allowed to anneal together by heating them to 95 degs for denaturation and allowing them to cool down and anneal overnight.
Friday, August 13
- Restriction digest of dif XP
After annealing the two strands, the oligo was cut with XbaI and PstI to obtain overhangs that would later ligate with the compatible overhangs of a digested vector.
- PCR purification of the digested dif XP
The digested oligo was PCR purified in order to get rid of any contaminants. PCR purification gets rid of short pieces of DNA which are less than about 40 base pairs.
- Gel Analysis of dif XP
Week 7
<html> <table width="1000px" border="0">
<tr> <td style="background-color:#FFFF66"> <b>Week 7</b> </td>
<td style="background-color:#33ffff;"><b>Monday</b>
</td> <td style="background-color:#33ffff;"><b>Tuesday</b> </td> <td style="background-color:#33ffff;"><b>Wednesday</b> </td> <td style="background-color:#33ffff;"><b>Thursday</b> </td> <td style="background-color:#33ffff;"><b>Friday</b> </td> </tr> <tr> <td style="background-color:#FF6666;width:100px;text-align:top;"><b>Morning</b> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> <ul> <li>Restriction digestion of 5' ins [K143008] (using Eco and Spe)</li> <li>PCR amplification of vector backbone pSB1C3</li> </ul> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> <ul> <li>Gel analysis and extraction of 5' ins</li> <li>Gel purification of 5' ins</li> <li>Restriction digestion of pSB1C3 (using Eco and Pst)</li> <li>PCR purification of pSB1C3 after digestion</li> <li>Gel analysis of 5' ins, dif and pSB1C3 to work out ratios for ligation</li> <li>Restriction digestion of pveg promoter and RBS [K143053] (using Eco and Spe)</li> <li>Restriction digetion of SpecR-T [K143065] (using Xba and Pst)</li> </ul>
</td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> <ul> <li>Replica plating and colony PCR of transformed colonies (containing 5' dif in pSB1C3)</li> <li>Gel extraction and PCR purification of pveg and SpecR-T in preparation for ligations this afternoon</li> <li>Gel analysis of pveg , Spec-T and pSB1C3 in order to work out ratios for the ligation</li> </ul> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> <ul> <li>Transformation of overnight ligations: 5' ins, dif with pSB1C3 and pveg, SpecR-T and pSB1C3 </li> </ul>
</td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> <ul> <li>Replica plating and colony PCR of: 5' ins, dif with pSB1C3 and pveg, SpecR-T and pSB1C3 </li> </ul> </td> </tr>
<tr>
<td style="background-color:#ff6666;width:100px;text-align:top;"><b>Afternoon</b>
</td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> <ul> <li>PCR purification of PSB1C3 vector </li> </ul> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> <ul> <li>Ligation of 5' ins and dif with pSB1C3 - a bench ligation (1 hour) and an overnight ligation were set up </li> <li>Transformation of E.Coli with the bench ligated products</li> <li>Gel analysis and extraction of pveg and SpecR-T</li> </ul>
</td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> <ul> <li>Overnight ligation of pveg and SpecR-T with pSB1C3 </li> </ul> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> </td>
<td style="background-color:#ccccff;height:100px;width:200px;text-align:top;"> <ul> <li>Gel analysis of colony PCR products from the transformations</li> <li> Overnight annealing of diff PES (Synthesized oligo)</li> </ul> </td> </tr> </table> </html>
Monday, August 16
- Restriction digest of 5' ins [K143008]
K143008 is the 5' integration site for the PyrD vector. This will be used as a front insert together with the dif XP for the pSB1C3 vector.
- PCR amplification of pSB1C3
The pSB1C3 vector backbone from the registry was amplified with the use of SB3 and SB2a primers. Submission of parts to the registry requires them to be in a pSB1C3 vector therefore any parts to be submitted will be inserted into this vector.
- PCR purification of pSB1C3
The PCR amplified vector was purified in order to get rid of any contaminants. For example, short pieces of DNA like the primers.
Tuesday, August 17
- Gel extraction and purification of 5' ins ES
The digested 5' ins was first analyzed on the gel to verify it's size and then extracted for purification. The 5' ins was gel purified in order to extract only the relevant piece of DNA.
- Restriction digest of pSB1C3
The pSB1C3 vector was digested so that it would contain compatible overhangs for ligation with inserts.
- PCR purification of pSB1C3 EP
The digested pSB1C3 was re-purified in order to get rid of any contaminant DNA that arose during the digestion.
- Restriction digests of pveg and Spec-T
pveg (promoter and RBS) and Spec-T (Spectinomycin with a terminator) were digested in preparation for 3A assembly.
- Ligation of 5' ins (ES) and dif (XP) with pSB1C3 (EP)
The digested 5' ins and dif (the front inserts) were ligated overnight with pSB1C3 (the vector). A bench ligation and an overnight ligation were set up.
- Transformation of E.Coli with bench ligate
E.Coli was transformed via the chemical method using the bench ligate.
- Gel extraction and purification of pveg and Spec-T
Since these are both inserts they were gel extracted and purified. PCR purification is not carried out for inserts since they are small and would therefore be lost during the process.
Wednesday, August 18
- Replica plating and colony PCR of 5' ins and dif in pSB1C3 (bench ligation)
- Ligation of pveg (ES) and SpecR-T (XP) with pSB1C3 (EP)
pveg and SpecR-T (the front inserts) were ligated overnight with pSB1C3 (the vector).
Thursday, August 19
- Transformation of E.Coli with the overnights ligates
- 5' ins and dif in pSB1C3
- pveg and SpecR-T in pSB1C3
Friday, August 20
- Replica plating and colony PCR of both transformations from yesterday.
- Annealing the forward and reverse strands of the dif P ES oligo
The forward and reverse strands of the 3' dif Pme1 sites with XbaI and PstI restriction sites on either side have been synthesized separately. The synthesized fragments arrive in solid powder form. These were immediately diluted in ddH2O to obtain a stock concentration of 1 ng/ul. They were then allowed to anneal together by heating them to 95 degs for denaturation and allowing them to cool down and anneal overnight.
Week 8
Week 8 | Monday | Tuesday | Wednesday | Thursday | Friday | Saturday |
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AFTERNOON |
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Week 9
Week 8 | Monday | Tuesday | Wednesday | Thursday | Friday | |
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Week 7
Week 6 | Monday | Tuesday | Wednesday | Thursday | Friday |
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MORNING | Starting assembly of AmyE vector
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k64 and k70, k70 only, Spec and 5' PyrD diff |
Spec and 5' PyrD diff
k64 and k70. k70 only was discarded since this was purely for a baground check |
AFTERNOON |
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Week 8
Week 8 | Monday | Tuesday | Wednesday | Thursday | Friday | Saturday |
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MORNING |
Set up overnight ligations for standard assembly (BBA) and 3A cloning (3A) of dif P
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AFTERNOON |
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Backbone PCR of pSB1C3 using PFU (3rd attempt)
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Week 9
Week 8 | Monday | Tuesday | Wednesday | Thursday | Friday | |
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MORNING |
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AFTERNOON |
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