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

■Experiment
1st week (8.13 - 8.19)
2nd week (8.20 - 8.26)
3rd week (8.27 - 9. 2)
4th week (9. 3 - 9. 9)
5th week (9.10 - 9.16)
6th week (9.17 - 9.23)
7th week (9.24 - 9.30)


■Protocols
Plasmid DNA Purification
Genome DNA Purification
Restruction Enzyme Degestion
DNA Fragment Ligation
Transformation
Electrophoresis
LB Medium


■Assay
Device1 Assay
Device2 Assay
Device3 Assay

Experiment

■2nd week (8.20 - 8.26)

■22nd Aug
・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
milliQ 17.5 μl
DNA solution 28 μl
0.5 x K buffer 2.5 μl
BamHI 1 μl
SacI 1 μl Total 50 μl
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 was 35 ng/ μl.
Backbone plasmid was 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
Densitometry of fdh4AB.
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 fhd4AB no.1 was 123 ng/ μl.
no.2 was 110 ng/ μl/

・Digestion
1. Mixed following
milliQ 25.5 μl
DNA solution 20 μl
0.5 x K buffer 2.5 μl
BamHI 1 μl
SacI 1 μl Total 50 μl
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.
Results
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.