Team:TMU-Tokyo/Notebook/Experiment/2nd week (8.20 - 8.26)

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<Br>
<Br>
<Br>
<Br>
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<B><A Href="https://2012.igem.org/Team:TMU-Tokyo/Notebook/Protocol/">■Protocols</A></B><Br>
 
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Plasmid DNA Purification<Br>
 
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Genome DNA Purification<Br>
 
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Restruction Enzyme Degestion<Br>
 
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DNA Fragment Ligation<Br>
 
-
Transformation<Br>
 
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Electrophoresis<Br>
 
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LB Medium<Br>
 
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<Br>
 
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<Br>
 
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<B><A Href="https://2012.igem.org/Team:TMU-Tokyo/Notebook/Assay">■Assay</A></B><Br>
 
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Device1 Assay<Br>
 
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Device2 Assay<Br>
 
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Device3 Assay<Br>
 
-
 
Line 62: Line 47:
<Br>
<Br>
<p class="description3">
<p class="description3">
 +
<b>■21th August</b><br />
 +
(Construction of Device1)<Br>
 +
・Purification <i>Escherichia coli</i> genome DNA Densitometry of purified<Br>
 +
・PCR of insert (pfrm-frmR)<Br>
 +
・Preparation of 0.8 % Agarose Gel<Br>
 +
・Electrophoresis<Br>
 +
→Failure: because of too dilute bands<Br>
 +
・PCR of insert (pfrm-frmR)<Br>
 +
・Preparation of 0.8 % Agarose Gel<Br>
 +
<Br>
 +
<b>■22nd Aug</b><br />
<b>■22nd Aug</b><br />
-
<b>・Refine of PCR products of frmR</i><br />
+
(Construction of Device1)<Br>
 +
・Electrophoresis<Br>
 +
→Failure: because of no bands<Br>
 +
・PCR of insert (pfrm-frmR)<Br>
 +
・Preparation of 0.8 % Agarose Gel<Br>
 +
・Electrophoresis<Br>
 +
→Failure: because of not appropriate bands<Br>
 +
・PCR of vector (BBa_K299009)<Br>
 +
・Preparation of 0.8 % Agarose Gel<Br>
 +
・Electrophoresis<Br>
 +
→<b>Success: We observed appropriate bands!</b><Br>
 +
<Br>
 +
 
 +
<b>・Refine of PCR products of frmR</b><br />
Mixed 1 volume of sample with 2 volumes of Buffer NT.<br />
Mixed 1 volume of sample with 2 volumes of Buffer NT.<br />
Placed a NucleoSpin Extract II Column into a Collection Tube and loaded the sample. Centrifuged for 30 seconds at 11,000 x g. Discarded flow-through and placed the column back into the collection tube.<br />
Placed a NucleoSpin Extract II Column into a Collection Tube and loaded the sample. Centrifuged for 30 seconds at 11,000 x g. Discarded flow-through and placed the column back into the collection tube.<br />
Line 70: Line 79:
Placed the NucleoSpin Extract II Column into a new 1.5 ml microcentrifuge tube. Added 50 μl Buffer NE and incubated at room temperature for 1 minute. Centrifuged for 1 minute at 11,000x g.<br />
Placed the NucleoSpin Extract II Column into a new 1.5 ml microcentrifuge tube. Added 50 μl Buffer NE and incubated at room temperature for 1 minute. Centrifuged for 1 minute at 11,000x g.<br />
<br />
<br />
-
Digestion<br />
+
<b>・Digestion</b><br />
-
1. Mixed following<br />
+
1. Mixed following: total 50µL<br />
-
milliQ 17.5 μl<br />
+
(milliQ 17.5µL / DNA solution 28µL / 0.5x K buffe 2.5µL / BamHI 1µL / SacI 1µL)<br />
-
DNA solution 28 μl<br />
+
2. Incubated for 1 hour at 37 °C.<br />
-
0.5 x K buffer 2.5 μl<br />
+
-
BamHI 1 μl<br />
+
-
SacI 1 μl
+
-
Total 50 μl
+
<br />
<br />
-
Incubated for 1 hour at 37 °C.<br />
+
<Br>
-
<br />
+
<b>■23rd Aug</b><br />
-
23rd Aug<br />
+
<b>・Refine of frmR and backbone plasmid</b><br />
-
Refine of frmR and backbone plasmid.<br />
+
Mixed 1 volume of sample with 2 volumes of Buffer NT.<br />
Mixed 1 volume of sample with 2 volumes of Buffer NT.<br />
Placed a NucleoSpin Extract II Column into a Collection Tube and loaded the sample. Centrifuged for 30 seconds at 11,000 x g. Discarded flow-through and placed the column back into the collection tube.<br />
Placed a NucleoSpin Extract II Column into a Collection Tube and loaded the sample. Centrifuged for 30 seconds at 11,000 x g. Discarded flow-through and placed the column back into the collection tube.<br />
Line 89: Line 93:
Placed the NucleoSpin Extract II Column into a new 1.5 ml microcentrifuge tube. Added 40 μl Buffer NE and incubated at room temperature for 1 minute. Centrifuged for 1 minute at 11,000 x g.<br />
Placed the NucleoSpin Extract II Column into a new 1.5 ml microcentrifuge tube. Added 40 μl Buffer NE and incubated at room temperature for 1 minute. Centrifuged for 1 minute at 11,000 x g.<br />
<br />
<br />
-
Densitometry<br />
+
<b>・Densitometry</b><br />
Diluted DNA samples 50 times with a solvent.<br />
Diluted DNA samples 50 times with a solvent.<br />
Turned on the machine; GeneQuant 100.<br />
Turned on the machine; GeneQuant 100.<br />
Line 96: Line 100:
Measured the concentration. <br />
Measured the concentration. <br />
<br />
<br />
-
Results<br />
+
<b>・Results</b><br />
-
Concentration of frmR was 35 ng/ μl.<br />
+
Concentration of frmR: 35 ng/ µL.<br />
-
Backbone plasmid was 105 ng/ μl.<br />
+
Backbone plasmid: 105 ng/ µL.<br />
<br />
<br />
-
Electrophoresis<br />
+
<b>・Electrophoresis</b><br />
Put an agalose gel into the tank, and poured TBE buffer.<br />
Put an agalose gel into the tank, and poured TBE buffer.<br />
Mixed DNA samples: loading buffer = 9: 1. Loaded samples into wells.<br />
Mixed DNA samples: loading buffer = 9: 1. Loaded samples into wells.<br />
Electrophoresed, stopped when samples move to 2/3.<br />
Electrophoresed, stopped when samples move to 2/3.<br />
<br />
<br />
-
Results<br />
+
<b>・Results</b><br />
We couldn’t obtain the target band of frmR.<br />
We couldn’t obtain the target band of frmR.<br />
<br />
<br />
-
24th Aug<br />
+
<Br>
-
Densitometry of fdh4AB.<br />
+
<b>■24th Aug</b><br />
-
Diluted DNA samples 50 times with a solvent.<br />
+
(Construction of Device1)<Br>
-
Turned on the machine; GeneQuant 100.<br />
+
・PCR of insert (pfrm-frmR)<Br>
-
Poured the solvent 100 μl into a cuvette and adjusted 0.<br />
+
・Preparation of 0.8 % Agarose Gel<Br>
-
Threw the solvent, poured the DNA sample.<br />
+
・Electrophoresis<Br>
-
Measured the concentration. <br />
+
→<b>Success: We observed appropriate bands but a lot of smere.</b><Br>
-
<br />
+
・Gradient PCR of insert (pfrm-frmR)<Br>
-
Results<br />
+
<Br>
-
Concentration of fhd4AB no.1 was 123 ng/ μl.<br />
+
<Br>
-
no.2 was 110 ng/ μl/<br />
+
<b>・Densitometry of fdh4AB PCR product.</b><br />
 +
1. Diluted DNA samples 50 times with a solvent.<br />
 +
2. Turned on the machine; GeneQuant 100.<br />
 +
3. Poured the solvent 100 μl into a cuvette and adjusted 0.<br />
 +
4. Threw the solvent, poured the DNA sample.<br />
 +
5. Measured the concentration. <br />
<br />
<br />
-
Digestion<br />
+
<b>・Results</b><br />
-
1. Mixed following<br />
+
Concentration of fhd4AB no.1: 123 ng/ µL, no.2: 110 ng/ µL/<br />
-
milliQ 25.5 μl<br />
+
-
DNA solution 20 μl<br />
+
-
0.5 x K buffer 2.5 μl<br />
+
-
BamHI 1 μl<br />
+
-
SacI 1 μl
+
-
Total 50 μl
+
<br />
<br />
 +
<b>・Digestion</b><br />
 +
1. Mixed following: total 50µL<br />
 +
(milliQ 25.5µL / DNA solution 20µL / 0.5x K buffe 2.5µL / BamHI 1µL / SacI 1µL)<br />
2. Incubated at 37 °C for 2.5 hours.<br />
2. Incubated at 37 °C for 2.5 hours.<br />
<br />
<br />
-
Electrophoresis of digestion products.<br />
+
<b>・Electrophoresis of digestion products</b><br />
Put an agalose gel into the tank, and poured TBE buffer.<br />
Put an agalose gel into the tank, and poured TBE buffer.<br />
Mixed DNA samples: loading buffer = 9: 1. Loaded samples into wells.<br />
Mixed DNA samples: loading buffer = 9: 1. Loaded samples into wells.<br />
Electrophoresed, stopped when samples move to 2/3.<br />
Electrophoresed, stopped when samples move to 2/3.<br />
<br />
<br />
-
Results<br />
+
<b>・Results</b><br />
We couldn’t obtain the target bands.<br />
We couldn’t obtain the target bands.<br />
 +
We run electrophoresis for the samples of before digestion, but we couldn’t obtain the target bands.<br />
<br />
<br />
-
We run electrophoresis for the samples of before digestion.<br />
+
<Br>
-
Results<br />
+
<b>■25th Aug</b><br />
-
We couldn’t obtain the target bands.<br />
+
<b>・Electrophoresis of gradient PCR products of fdh4AB</b><br />
-
<br />
+
-
25th Aug<br />
+
-
Electrophoresis of gradient PCR products of fdh4AB.<br />
+
Put an agalose gel into the tank, and poured TBE buffer.<br />
Put an agalose gel into the tank, and poured TBE buffer.<br />
Mixed DNA samples: loading buffer = 9: 1. Loaded samples into wells.<br />
Mixed DNA samples: loading buffer = 9: 1. Loaded samples into wells.<br />
Line 159: Line 163:
55.0 C<br />
55.0 C<br />
<br />
<br />
-
Results<br />
+
<b>・Results</b><br />
We obtained the target bands from F, G and H. Also E showed a weak band. These data showed that better annealing temperature was 55.0 – 58.0 C.<br />
We obtained the target bands from F, G and H. Also E showed a weak band. These data showed that better annealing temperature was 55.0 – 58.0 C.<br />
<br />
<br />

Latest revision as of 15:32, 26 September 2012

 


Experiment



■2nd week (8.20 - 8.26)


■21th August
(Construction of Device1)
・Purification Escherichia coli genome DNA Densitometry of purified
・PCR of insert (pfrm-frmR)
・Preparation of 0.8 % Agarose Gel
・Electrophoresis
→Failure: because of too dilute bands
・PCR of insert (pfrm-frmR)
・Preparation of 0.8 % Agarose Gel

■22nd Aug
(Construction of Device1)
・Electrophoresis
→Failure: because of no bands
・PCR of insert (pfrm-frmR)
・Preparation of 0.8 % Agarose Gel
・Electrophoresis
→Failure: because of not appropriate bands
・PCR of vector (BBa_K299009)
・Preparation of 0.8 % Agarose Gel
・Electrophoresis
Success: We observed appropriate bands!

・Refine of PCR products of frmR
Mixed 1 volume of sample with 2 volumes of Buffer NT.
Placed a NucleoSpin Extract II Column into a Collection Tube and loaded the sample. Centrifuged for 30 seconds at 11,000 x g. Discarded flow-through and placed the column back into the collection tube.
Added 700 μl Buffer NT3 to the NucleoSpin Extract II Column. Centrifuged for 30 seconds at 11,000 x g. Discarded flow-though and placed the column back into the collection tube.
Centrifuged for 1 minute at 11,000 x g to remove Buffer NT3 completely.
Placed the NucleoSpin Extract II Column into a new 1.5 ml microcentrifuge tube. Added 50 μl Buffer NE and incubated at room temperature for 1 minute. Centrifuged for 1 minute at 11,000x g.

・Digestion
1. Mixed following: total 50µL
(milliQ 17.5µL / DNA solution 28µL / 0.5x K buffe 2.5µL / BamHI 1µL / SacI 1µL)
2. Incubated for 1 hour at 37 °C.


■23rd Aug
・Refine of frmR and backbone plasmid
Mixed 1 volume of sample with 2 volumes of Buffer NT.
Placed a NucleoSpin Extract II Column into a Collection Tube and loaded the sample. Centrifuged for 30 seconds at 11,000 x g. Discarded flow-through and placed the column back into the collection tube.
Added 700 μl Buffer NT3 to the NucleoSpin Extract II Column. Centrifuged for 30 seconds at 11,000 x g. Discarded flow-though and placed the column back into the collection tube.
Centrifuged for 1 minute at 11,000 x g to remove Buffer NT3 completely.
Placed the NucleoSpin Extract II Column into a new 1.5 ml microcentrifuge tube. Added 40 μl Buffer NE and incubated at room temperature for 1 minute. Centrifuged for 1 minute at 11,000 x g.

・Densitometry
Diluted DNA samples 50 times with a solvent.
Turned on the machine; GeneQuant 100.
Poured the solvent 100 μl into a cuvette and adjusted 0.
Threw the solvent, poured the DNA sample.
Measured the concentration.

・Results
Concentration of frmR: 35 ng/ µL.
Backbone plasmid: 105 ng/ µL.

・Electrophoresis
Put an agalose gel into the tank, and poured TBE buffer.
Mixed DNA samples: loading buffer = 9: 1. Loaded samples into wells.
Electrophoresed, stopped when samples move to 2/3.

・Results
We couldn’t obtain the target band of frmR.


■24th Aug
(Construction of Device1)
・PCR of insert (pfrm-frmR)
・Preparation of 0.8 % Agarose Gel
・Electrophoresis
Success: We observed appropriate bands but a lot of smere.
・Gradient PCR of insert (pfrm-frmR)


・Densitometry of fdh4AB PCR product.
1. Diluted DNA samples 50 times with a solvent.
2. Turned on the machine; GeneQuant 100.
3. Poured the solvent 100 μl into a cuvette and adjusted 0.
4. Threw the solvent, poured the DNA sample.
5. Measured the concentration.

・Results
Concentration of fhd4AB no.1: 123 ng/ µL, no.2: 110 ng/ µL/

・Digestion
1. Mixed following: total 50µL
(milliQ 25.5µL / DNA solution 20µL / 0.5x K buffe 2.5µL / BamHI 1µL / SacI 1µL)
2. Incubated at 37 °C for 2.5 hours.

・Electrophoresis of digestion products
Put an agalose gel into the tank, and poured TBE buffer.
Mixed DNA samples: loading buffer = 9: 1. Loaded samples into wells.
Electrophoresed, stopped when samples move to 2/3.

・Results
We couldn’t obtain the target bands.
We run electrophoresis for the samples of before digestion, but we couldn’t obtain the target bands.


■25th Aug
・Electrophoresis of gradient PCR products of fdh4AB
Put an agalose gel into the tank, and poured TBE buffer.
Mixed DNA samples: loading buffer = 9: 1. Loaded samples into wells.
Electrophoresed, stopped when samples move to 2/3.

Samples
68 C
67.1 C
65.5 C
63.1 C
60.1 C
58.0 C
56.2 C
55.0 C

・Results
We obtained the target bands from F, G and H. Also E showed a weak band. These data showed that better annealing temperature was 55.0 – 58.0 C.