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Team:Warsaw/Calendar-Main/8 July 2009
From 2009.igem.org
(Difference between revisions)
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<li>uncut plasmid (isolate no.3)</li> | <li>uncut plasmid (isolate no.3)</li> | ||
<li>cut plasmid (isolate no.3)</li> | <li>cut plasmid (isolate no.3)</li> | ||
| - | |||
</ol> | </ol> | ||
| - | <ul> | + | </ol> |
| + | </ul> | ||
<br /> | <br /> | ||
<br /> | <br /> | ||
<p>Note: isolate no.1 contains a correctly inserted PCR product</p> | <p>Note: isolate no.1 contains a correctly inserted PCR product</p> | ||
| + | <br /> | ||
| + | </html> | ||
| + | <!-- TU EDYTOWALA ANIA prosze nie szatkowac znacznikami! --> | ||
| + | <html> | ||
| + | <h3>Miecznikowa team Aim: debug RFP-terminator ligation that did not work<h3> | ||
| + | <h4>Jarek/Franek/Ania</h4> | ||
| + | <p>Task1:</p> | ||
| + | <ul> | ||
| + | <li>Alkaline lysis of the plasmid containing Terminator</li> | ||
| + | </ul> | ||
| + | <br /> | ||
| + | <p>Methods:</p> | ||
| + | <ul><li><p>PlasmidMini set by A&A Biotechnology was used. 2 test tubes with 5ml LB and 5 ul Ampicyline were first inoculated with the plasmid containing colonies. The cultures were incubated over night at 37C.Alkaline lysis was performed on both cultures. The pellet from 5 ml of bacteria was used. | ||
| + | </li> | ||
| + | </ul> | ||
| + | <p>Results:</p> | ||
| + | <ul> | ||
| + | <li>DNA extraction quality controll.DNA Concentration was measured using Spectrophotometer NanoDrop ND-1000 | ||
| + | </li> | ||
| + | </ul> | ||
</html> | </html> | ||
| + | {| class="wikitable" style="text-align:center; width:400px; height:90px; border-collapse: collapse; border: 1px dashed blue; margin: 1em auto 1em auto" border="1" | ||
| + | |- | ||
| + | ! DNA sample | ||
| + | ! DNA concentration in ng | ||
| + | |- | ||
| + | | Terminator sample 1 (Ter1) | ||
| + | | 73.9 ng/ul | ||
| + | |- | ||
| + | | Terminator sample 1 (Ter2) | ||
| + | | 85.46 ng/ul | ||
| + | |} | ||
| + | <html> | ||
| + | <p>Task2:</p> | ||
| + | <ul> | ||
| + | <li>We decided to measure the concentration of DNA in our samples for future use e.g. efficient ligation mix. NanoDrop ND-1000 was used.</li> | ||
| + | </ul> | ||
| + | <br /> | ||
| + | <p>Results:</p> | ||
| + | </html> | ||
| + | {| class="wikitable" style=" text-align:center; width:400px; height:300px; border-collapse: collapse; border: 1px dashed blue; margin: 1em auto 1em auto" border="1" | ||
| + | |- | ||
| + | ! DNA sample | ||
| + | ! DNA concentration in ng | ||
| + | |- | ||
| + | | Rfp3 1st measurement | ||
| + | | 17.49 ng/ul | ||
| + | |- | ||
| + | | Rfp3 2nd | ||
| + | | 24.18 ng/ul | ||
| + | |- | ||
| + | | Rfp3 3rd | ||
| + | | 24.50 ng/ul | ||
| + | |- | ||
| + | | Rfp4 1st measurement | ||
| + | | 28.85 ng/ul | ||
| + | |- | ||
| + | | Rfptra (digested plasmid with RFP) | ||
| + | | 0.4 ng/ul | ||
| + | |- | ||
| + | | Rfptra 2nd measurement | ||
| + | | 0.8 ng/ul | ||
| + | |- | ||
| + | | RBS digested (digested RBS) | ||
| + | | 1.44 ng/ul | ||
| + | |- | ||
| + | | RBS digested 2nd measurement | ||
| + | | 0.72 ng/ul | ||
| + | |} | ||
| + | <html> | ||
| + | <p>Notes - IMPORTANT:</p> | ||
| + | <ul> | ||
| + | <li>Rfptra and RBSdigested samples were extracted from the gel using gel-out kit by A&ABiotechnology. Presented data shows that after gel extraction there is very little DNA in the sample. Probably there is a ****problem with gel extraction procedure**** - the Gel-out set by A&A Biotechnology might be defective. | ||
| + | </li> | ||
| + | </ul> | ||
| + | </html> | ||
| + | |||
| + | |||
| + | |||
| + | |||
Revision as of 21:35, 8 July 2009
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Gradient PCR Pho
Kama
Kama
Tasks:
- Amplification of phoP/phoQ
Methods:
PCR mixture's composition:
1ul pfu buffer (Fermentas), 1ul MgSO4 (Fermentas), 0,5ul primers, 0,5ul dNTPs (10 mM), 0,25ul pfu turbo polymerase, 0,5ul template DNA from Listeria, optionally: 0,75ul DMSO, solution was topped up with H2O to 10ul.
- PCR programs:
pho
4min 95°C
(30s 95°C, 1min 45-55°C, 4min 72°C)x3
(30s 95°C, 1min 55-60°C, 4min 72°C)x28
10min 72°C
~ 7°C
- Electrophoretic separation on 1% agarose gel
Results:
- Gel (from left)
- control -
- 2-6 - samples (annealing temperature increases to from the left to the right)
- 7-11 - samples with DMSO (annealing temperature increases to from the left to the right)
- M - GeneRuler DNA Ladder Mix #SM0333 (Fermentas)
Notes:
Isolation and digest of pKS-CRO (ligated and transformed into E. coli the previous day)
Kuba
- pKS-CRO cut with XbaI and EcoRI
.JPG)
- Gel (from the left)
- GeneRuler DNA Ladder Mix #SM0333 (Fermentas)
- uncut plasmid (isolate no.1)
- cut plasmid (isolate no.1)
- uncut plasmid (isolate no.2)
- cut plasmid (isolate no.2)
- uncut plasmid (isolate no.3)
- cut plasmid (isolate no.3)
Note: isolate no.1 contains a correctly inserted PCR product
Miecznikowa team Aim: debug RFP-terminator ligation that did not work
Jarek/Franek/Ania
Jarek/Franek/Ania
Task1:
- Alkaline lysis of the plasmid containing Terminator
Methods:
PlasmidMini set by A&A Biotechnology was used. 2 test tubes with 5ml LB and 5 ul Ampicyline were first inoculated with the plasmid containing colonies. The cultures were incubated over night at 37C.Alkaline lysis was performed on both cultures. The pellet from 5 ml of bacteria was used.
Results:
- DNA extraction quality controll.DNA Concentration was measured using Spectrophotometer NanoDrop ND-1000
| DNA sample | DNA concentration in ng |
|---|---|
| Terminator sample 1 (Ter1) | 73.9 ng/ul |
| Terminator sample 1 (Ter2) | 85.46 ng/ul |
Task2:
- We decided to measure the concentration of DNA in our samples for future use e.g. efficient ligation mix. NanoDrop ND-1000 was used.
Results:
| DNA sample | DNA concentration in ng |
|---|---|
| Rfp3 1st measurement | 17.49 ng/ul |
| Rfp3 2nd | 24.18 ng/ul |
| Rfp3 3rd | 24.50 ng/ul |
| Rfp4 1st measurement | 28.85 ng/ul |
| Rfptra (digested plasmid with RFP) | 0.4 ng/ul |
| Rfptra 2nd measurement | 0.8 ng/ul |
| RBS digested (digested RBS) | 1.44 ng/ul |
| RBS digested 2nd measurement | 0.72 ng/ul |
Notes - IMPORTANT:
- Rfptra and RBSdigested samples were extracted from the gel using gel-out kit by A&ABiotechnology. Presented data shows that after gel extraction there is very little DNA in the sample. Probably there is a ****problem with gel extraction procedure**** - the Gel-out set by A&A Biotechnology might be defective.
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