Team:HokkaidoU Japan/Notebook/aggregation Week 4

From 2012.igem.org

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====Plasmid extraction====
====Plasmid extraction====
Plasmid extraction for Ag43(resuspended colony incubated at July 17th and resuspended  colony incubated at July 20th). We used FastGene Plasmid Mini Kit(Nippon Genetics) and got 50 ul of DNA solutions.  
Plasmid extraction for Ag43(resuspended colony incubated at July 17th and resuspended  colony incubated at July 20th). We used FastGene Plasmid Mini Kit(Nippon Genetics) and got 50 ul of DNA solutions.  
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===July 24th===
===July 24th===
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======Electrophoresis======
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=====Electrophoresis=====
Electrophoresis for Ag43(plasmid extraction at July 23rd) and Ag43 digestion results(digested with EcoRI and SpeI)
Electrophoresis for Ag43(plasmid extraction at July 23rd) and Ag43 digestion results(digested with EcoRI and SpeI)
[[image:HokkaidoU2012 120724 ag43-dt pcr.jpg|thumb|Plasmid extraction result]]
[[image:HokkaidoU2012 120724 ag43-dt pcr.jpg|thumb|Plasmid extraction result]]
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[[image:HokkaidoU2012 120726 digestion ligation.jpg|thumb|Digestion and Ligation results]]
[[image:HokkaidoU2012 120726 digestion ligation.jpg|thumb|Digestion and Ligation results]]
There are no band in the lane of ligation products. But if digestion products were not ligated, two bands of digestion products would exist in the lane.   
There are no band in the lane of ligation products. But if digestion products were not ligated, two bands of digestion products would exist in the lane.   
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I could not understand what is happend.
I could not understand what is happend.
I tried it again, but the result was the same.
I tried it again, but the result was the same.
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Latest revision as of 03:18, 27 September 2012

Contents

July 23rd

Plasmid extraction

Plasmid extraction for Ag43(resuspended colony incubated at July 17th and resuspended colony incubated at July 20th). We used FastGene Plasmid Mini Kit(Nippon Genetics) and got 50 ul of DNA solutions.


July 24th

Electrophoresis

Electrophoresis for Ag43(plasmid extraction at July 23rd) and Ag43 digestion results(digested with EcoRI and SpeI)

Plasmid extraction result
Digestion result

From this digestion result, we found out that one or two enzymes didn't work successfully but there are enough concentration of DNA in 3000bp band to use for digestion.

Gel extraction

Gel extraction for digestion production. We used FastGene Gel&PCR extraction kit(NipponGenetics)and got 50 ul of DNA solution.

Ethanol precipitation

Ethanol precipitation for digestion and gel extraction product.

  1. Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
  2. Centrifuged at 15000 rpm, 10min at 4C.
  3. Removed supernatant and added 220 ul of 70% ethanol.
  4. Centrifuged at 15000 rpm, 10 min at 4C.
  5. Removed supernatant and dried out at room temperature after that added 10 ul of DW.
Ethanol precipitation result

From this result, we estimated that the concentration of ethanol precipitation product is about 40 ng/ul.

Digestion

Digestion to confirm how many PstI cutting sites are there in K346007 and for Ag43-dT complex with SpeI and XbaI.
Ag43 PstI

DNA solution 5 ul
PstI 1 ul
10xH buffer 2 ul
DW 12 ul
Total 20 ul


Ag43-dT
SpeI and XbaI

DNA solution 12 ul
SpeI 1 ul
XbaI 1 ul
10xH buffer 2 ul
DW 4 ul
Total 20 ul


Electrophoresis

Ag43 d+(P) Digestion result
Ag43-dT d+(X&S) Digestion result

Electrophoresis for digestion results.

From this result, we found that there are 6 PstI cutting sites in K346007(Ag43).

Gel extraction

Gel extraction of Ag43-dt digestion result. We used FastGene Gel&PCR extraction kit(NipponGenetics)and got 50 ul of DNA solution.

Digestion

Ag43-dT and pSB1AK3 mixture solution(each DNA fragment is about 3kbp) digested with HindIII to digest pSB1AK3.

DNA solution 8 ul
HindIII 1 ul
10xM buffer 1 ul
Total 10 ul


July 25th

Digestion

Digestion of pT7-RBS on pSB1K3 with SpeI.

DNA solution 3 ul
SpeI 1 ul
10xH buffer 1 ul
DW 5 ul
Total 10 ul
Digestion result(Ag43-dT and pT7-RBS)

We were confirmed that pSB1AK3 was digested and became 1.3k and 1.8k bp fragments by HindIII.

Gel extraction

Gel extraction of Ag43-dT on pSB1AK3(HindIII) and pT7-RBS on pSB1K3(SpeI). We used FastGene Gel&PCR extraction kit(NipponGenetics)and got 50 ul of DNA solution.

Ethanol precipitation

Ethanol precipitation of digestion and gel extraction products.

  1. Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
  2. Centrifuged at 15000 rpm, 10 min at 4C.
  3. Removed supernatant and added 220 ul of 70% ethanol.
  4. Centrifuged at 15000 rpm, 5 min at 4C.
  5. Removed supernatant and dried out at room temperature after that added 5 ul of DW.

Ligation

Ligation for pT7-RBS on pSB1K3(Vector) and Ag43-dT(Insert).

pT7-RBS on pSB1K3 2 ul
Ag43-dT 2 ul
DW 1 ul
Ligation Mighty Mix(TAKARA) 5 ul
Total 10 ul


Degree Minute
16 30
65 10
4 Hold


July 26th

Transformation

Transformation plasmid DNA ligated at 25th (pT7-RBS-Ag43-dT on pSB1K3) into BL21.

  1. Added 2 ul of plasmid DNA to 50 ul of thawed competent cells on ice.
  2. Incubated on ice for 30 min.
  3. Added 200 ul of LB then incubated the cells for 2 hrs at 37C.
  4. Prepared and Labeled two petri dishes with LBK.
  5. Spread 200 ul of the transformation onto first dish.
  6. Added 450 ul of LB to 50 ul of the transformation and spread 200 ul of it onto second dish.
  7. Incubated the plates at 37C for over 30 hrs.

There were no colony on the plates.

Electrophoresis

Electrophoresis of digestion and ligation products.

  1. Placed TBE agarose gel in Electrophoresis chamber.
  2. Added 1/2X TBE buffer to Electrophoresis chamber.
  3. Added 5 ul of EtBr and ran at 100 V for 30 min.
  4. Apply 1kb DNA ladder and each samples.
  5. Ran at 100 V for 30 min.
Digestion and Ligation results

There are no band in the lane of ligation products. But if digestion products were not ligated, two bands of digestion products would exist in the lane.


July 27th

Transformation

Transformation plasmid DNA ligated at 25th (pT7-RBS-Ag43-dT on pSB1K3) into BL21.

  1. Added 2 ul of plasmid DNA to 50 ul of thawed competent cells on ice.
  2. Incubated on ice for 30 min.
  3. Added 600 ul of LB then incubated the cells for 2 hrs at 37C.
  4. Prepared and Labeled three petri dishes with LBK X2 and LBC.
  5. Spread 300 ul of the transformation onto LBK dish.
  6. Added 900 ul of LB to 100 ul of the transformation and spread 300 ul of it onto LBC dish and LBK dish.
  7. Incubated the plates at 37C for 17 hrs and 30 min.

Ligation

Ligation of pT7-RBS on pSB1K3(Vector) and Ag43-dT(Insert)

pT7-RBS on pSB1K3 2 ul
Ag43-dT 2 ul
DW 1 ul
Ligation Mighty Mix(TAKARA) 5 ul
Total 10 ul


Degree Minute
16 30
65 10
4 Hold


July 28th

Transformation result left:LBC center:LBK right:LBK

There were many colonies on LBC. We guessed we mistook pT7-RBS on pSB1C3 for pT7-RBS on pSB1K3.

Liquid culture

Liquid culture for pT7-RBS-Ag43-dT on pSB1C3.

  1. Added 2 ml of LBC into culture tubes.
  2. Resuspended 5 colonies.
  3. Incubated the tubes at 30C for 22 hrs.

Digestion

Digestion of pT7-RBS on pSB1K3 with SpeI and Ag43-dT on pSB1AK3(cut with SpeI & XbaI) with HindIII.
pT7-RBS on pSB1K3

DNA solution 3 ul
SpeI 1 ul
10xH buffer 1 ul
DW 5 ul
Total 10 ul

Ag43-dT on pSB1AK3(cut with SpeI & XbaI)

DNA solution 8 ul
HindIII 1 ul
10xM buffer 1 ul
Total 10 ul

Digested at 37C for 2 hrs.

digestion result

This results showed that pSB1AK3 was successfully digested into fragments(1.3K and 1.8K bp), but we couldn't confirm whether pT7-RBS on pSB1K3 was digested or not.

Gel extraction

Gel extraction for digestion production. We used FastGene Gel&PCR extraction kit(NipponGenetics) and got 50 ul of DNA solution.

Ethanol precipitation

Ethanol precipitation for digestion and gel extraction product.

  1. Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
  2. Centrifuged at 15000 rpm, 10 min at 4C.
  3. Removed supernatant and added 220 ul of 70% ethanol.
  4. Centrifuged at 15000 rpm, 10 min at 4C.
  5. Removed supernatant and dryed out at room temperature after that added 10 ul of DW.

Ligation

Ligation of pT7-RBS on pSB1K3(Vector) and Ag43-dT(Insert)

pT7-RBS on pSB1K3 2 ul
Ag43-dT 2 ul
DW 1 ul
Ligation Mighty Mix(TAKARA) 5 ul
Total 10 ul


Degree Minute
16 30
65 10
4 Hold


July 29th

Plasmid extraction

Plasmid extraction for 5 cultures of pT7-RBS-Ag43-dT. We used FastGene Plasmid Mini Kit(Nippon Genetics) and got 50 ul of DNA solutions.

Plasmid extraction products

Digestion

We need to confirm the DNA is pT7-RBS-Ag43-dT or not.
Plasmid extraction products(pT7-RBS-Ag43-dT) PstI

DNA solution 4 ul
PstI 1 ul
10xH buffer 2 ul
DW 13 ul
Total 20 ul


Plasmid extraction products(pT7-RBS-Ag43-dT)
EcoR1 and Spe1

DNA solution 4 ul
EcoR1 1 ul
Spe1 1 ul
10xH buffer 2 ul
DW 12 ul
Total 20 ul

Electrophoresis

Electrophoresis for digestion results.

Digestion result

I could not understand what is happend. I tried it again, but the result was the same.



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