Team:TzuChiU Formosa/Protocol

From 2009.igem.org

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https://static.igem.org/mediawiki/2009/e/ea/Project.jpg
https://static.igem.org/mediawiki/2009/e/ea/Project.jpg
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====Tansformation Protocol ====
+
A. Culture CP919
 +
 
 +
B. Put Aqueorin-GFP into plasmid .
 +
 
 +
C. Transform the cp919 into the Midnight Apollo!
 +
 
 +
D. Sense the light.
 +
 
 +
E. In the dark,  the Midnight Apollo! is activated and emit the light.
-
#Take the cp919 competent cell eppendorf from -80℃ freezer.
 
-
#Add 4ul plasmid to competent cell and place at ice for 30 minutes.
 
-
#Put the eppendorf into 42℃ water bath for 90 seconds.
 
-
#Place the eppendorf at ice for 2 minutes.
 
-
#Add 1ml LBM to the eppendorf and well mixed.
 
-
#Put the eppendorf into 37℃ water bath incubate for an hour.
 
-
#Centrifuged at 7000 r.p.m for 5 minutes and remove some supernatant liquid.
 
-
#Spread antibiotic which we need on plate. When the plate dry, spread appropriate the culture liquid on plate.
 
-
#Incubate into 37℃ water bath for 16~18 hours.
 
====Competent Cell (CP919-Cph8)====
====Competent Cell (CP919-Cph8)====
-
#Day1. Streak out the E.coli strain on an LBM plate (with kanamycin antibiotic) to isolate colonies and incubate at 37℃ overnight (16-20 hours).
+
#Day1. Streak out the E.coli strain on an LB plate (with kanamycin)and incubate at 37℃ overnight (16-20 hours).
-
#Day2. Select a single colony and inoculate 10 ml sterile LBM Grow overnight (16-20 hours) in a 37℃ shaker incubator.
+
#Day2. Select a single colony and inoculate 10 ml sterile LB and grow overnight (16-20 hours) in a 37℃ shaker incubator.
-
#Day3. Add 2ml overnight culture to 250ml flask which with 100 ml sterile LBM.
+
#Day3. Add 2ml overnight culture to 250ml flask containing 100 ml LB.
-
#Grow the cultures to OD600 = 0.2~0.4 (incubate about 75~90 min.).
+
#Grow the cultures to OD600 = 0.2~0.4 (incubate with shaking for 75~90 min.)
-
#Centrifuge, 4℃,3000 r.p.m,10 min.
+
#Spin down the bacteria at 4℃,3000 rpm for 10 min.
#Discard the supernatant and mix the cell pellet with 10ml FSB.
#Discard the supernatant and mix the cell pellet with 10ml FSB.
#Keep the cells on ice for 3~4 hours.
#Keep the cells on ice for 3~4 hours.
-
#Centrifuge, 4℃,3000 r.p.m,10 min.
+
#Spin down, at 4℃,3000 rpm for 10 min.
#Discard the supernatant and mix the cell pellet with 5ml FSB.
#Discard the supernatant and mix the cell pellet with 5ml FSB.
-
#Pipet 200μl of the cell suspension into sterile 1.5ml eppendorf. Freeze these tubes on N2 (aq.) and then transfer them to -80℃ freezer.
+
#Pipet 200μl of the cell suspension into sterile 1.5ml eppendorf tubes. Freeze these tubes in liquid nitrogen, then transfer them to -80℃ freezer.
-
====Real Time PCR====
+
 
 +
====Tansformation Protocol ====
 +
 
 +
#Take competent cell in an eppendorf tube from -80℃ freezer put in ice.
 +
#Add 2ul plasmid to competent cell and place in ice for 5 minutes.
 +
#Put the transformed cells into 42℃ water bath for 60 seconds.
 +
#Then place the cells in ice for 2 minutes.
 +
#Add 1ml LB to the cells and mixed.
 +
#Put the eppendorf tube in 37℃ water bath and incubate for an hour.
 +
#Spin down at 7000 rpm for 5 minutes and remove most of the supernatant.
 +
#While the cells are incubated at 37℃ water bath spread 100ul Ampicilin(50mg/ml) on the plate. When the plate is dried, spread bacteria on the plate.
 +
#Incubate at 37℃ incubater for 16~18 hours.
 +
 
-
1. Take ice for preparing.
+
==== PCR ====
-
2. dilution of concentration：
 
-
:'''2.1'''
+
1. Dissolve the primers in water to have the concentration of 10nM.
-
:template DNA（Omp R）：500 times diluted     
+
-
:499μl ddH2O ＋ 1μl omp R＝500μl
+
-
:'''2.2'''
 
-
:primer forward ＆ primer reverse（p88）：10 times diluted
 
-
:10μl p88 primer forward＋ 90μl ddH2O
 
-
3. Materials：
+
2. PCR reaction mixer：
      
      
   Template DNA（10ng/μl） 5
   Template DNA（10ng/μl） 5
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   Total 20 μl
   Total 20 μl
-
4. Step：
 
-
Meacure template DNA  2μl
 
-
Measure 10× PCR buffer  2μl
 
-
Measure 10× dNTP        2μl
 
-
Measure forward primer  0.5μl
 
-
Measure reverse  primer  0.5μl
 
-
Measure Pfu DNA polymerase  0.1μl
 
-
Follow this step ，puttng the reagent in the eppendorf.
 
-
5. Use the PCR to amplify our product：PCR program
+
3. Put the reaction mixer in a PCR tube.
-
 
+
4.The PCR program is as follow :
-
:'''5.1'''
+
:'''4.1'''
:94℃    30 seconds
:94℃    30 seconds
:60℃    30seconds
:60℃    30seconds
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-
:'''5.2'''
+
:'''4.2'''
:94℃    30 seconds
:94℃    30 seconds
:55℃    30seconds
:55℃    30seconds
:72℃    2 minutes
:72℃    2 minutes
:Cycle    34 times
:Cycle    34 times
-
:72℃    10 minutes
 
 +
Extend PCR product at 72℃ for 10 minutes
-
6. The PCR production separate by 1％ agar.
 
-
7. After separate using the EtBr to dye agar and exposing by UV.
+
5. The PCR product was examed by electrophoresis in 1％ agarose.
-
====T-A cloning protocol====
 
-
Take an eppendorf,and add these one by one,after mix well,overnight 4℃.
+
====T-A cloning====
 +
 
 +
 
 +
 
 +
 
 +
 
 +
Take an eppendorf tube and add following component one by one and mix well,incubated at 4℃ overnight.
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-
====Cloning PCR====
+
====Colony PCR(To verify the presence of our gene of interest)====
-
#Add 10μl cell, centrifuge 14000 rpm, 10 min
+
 
 +
 
 +
 
 +
 
 +
 
 +
#Take 10μl of bacterial culture, spin down at 14000 rpm for 10 min.
#Discard the supernatant
#Discard the supernatant
-
#Add 500μl ddH20, Votex
+
#Add 500μl ddH20, Vortex
-
#Boiling 20min, 100℃
+
#Boil for 20 min.
-
#Add 5μl DNA, 10x dNTP 2μl, 10x Buffer 2μl, forward primer（10μM）0.5μl reverse primer（10μM）0.5μl, Taq DNA polymerase 0.1μl, ddH20
+
#Take 5μl of above bacterial lysate, and add 10x dNTP 2μl, 10x Buffer 2μl, forward primer（10μM）0.5μl reverse primer（10μM）0.5μl, Taq DNA polymerase 0.1μl, ddH20
#Use the PCR to amplify our product：PCR program
#Use the PCR to amplify our product：PCR program
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   Cycle 34 times
   Cycle 34 times
   25℃ 2 min
   25℃ 2 min
-
　7. The PCR production separate by 1％ agar.  
+
　　7. The PCR product was examed by electrophoresis in 1％ agarose.
-
　8. After separate using the EtBr to dye agar and exposing by UV.
+
====Plasmid extraction(Homemade)====
 +
 
 +
 
 +
 
 +
 
 +
 
 +
#Transfer 1.5ml of bacterial culture to each well(24 wells plate)
 +
#pellet cells by centrifuging at 33000 rpm for 10min at 4℃
 +
#carefully remove the supernatant
 +
#add 100μl of Solution 1 (*)to each well, and vortex
 +
#add 200μl of Solution 2 (*)to each well, and mix gently
 +
#add 150μl of Solution 3 (*)to each well
 +
#spin down 3000rpm at 4℃  for 10min
 +
#add 1 ml 100% EtOH to new well
 +
#Transfer the supernatant to the new well, containing 100% EtOH.
 +
#spin down 3300rpm at 4℃ for 30min.
 +
#carefully remove the supernatant.
 +
#add 75% EtOH to wash pellets, then remove the supernantant, then air dry.
 +
#add 40μl ddH2O to each well, to dissolve with plasmid DNA
 +
#store the plate in 4℃
 +
  (*)Sol 1: 10m Miris/0.5mM HEDTA, PH 7.4 buffer.
 +
    Sol 2: 0.2N NaOH/1% SDS
 +
    Sol 3: 3M KOAC/HOAC
 +
 
 +
====Digestion====
 +
 
 +
 
 +
 
 +
 
 +
Digestion mixture
 +
 
 +
  DNA        20μl
 +
  10x buffer 3μl
 +
  Enzyme    1μl
 +
  RNase H2O  6μl
 +
  __________________________
 +
  Total      30μl
 +
3. The order for adding materials to wells is from plenty to less
 +
4. Place the plate in 37℃water bath overnight
 +
 
 +
 
 +
 
 +
====Ligation====
 +
 
 +
 
 +
 
 +
 
 +
 
 +
Take an eppendorf tube and add following component one by one and mix well,incubated at 16℃ overnight.
 +
 
 +
 
 +
  Insert(Aeq.-GFP) 7.5μl
 +
  Vector(pSB1A3)  5.5μl
 +
  10X ligase buffer 1μl
 +
  T4 DNA ligase  1μl
 +
  _________________________________
 +
  total 30μl

Latest revision as of 01:01, 22 October 2009


Contents

Protocol

Project.jpg

A. Culture CP919

B. Put Aqueorin-GFP into plasmid .

C. Transform the cp919 into the Midnight Apollo!

D. Sense the light.

E. In the dark, the Midnight Apollo! is activated and emit the light.


Competent Cell (CP919-Cph8)

  1. Day1. Streak out the E.coli strain on an LB plate (with kanamycin)and incubate at 37℃ overnight (16-20 hours).
  2. Day2. Select a single colony and inoculate 10 ml sterile LB and grow overnight (16-20 hours) in a 37℃ shaker incubator.
  3. Day3. Add 2ml overnight culture to 250ml flask containing 100 ml LB.
  4. Grow the cultures to OD600 = 0.2~0.4 (incubate with shaking for 75~90 min.)
  5. Spin down the bacteria at 4℃,3000 rpm for 10 min.
  6. Discard the supernatant and mix the cell pellet with 10ml FSB.
  7. Keep the cells on ice for 3~4 hours.
  8. Spin down, at 4℃,3000 rpm for 10 min.
  9. Discard the supernatant and mix the cell pellet with 5ml FSB.
  10. Pipet 200μl of the cell suspension into sterile 1.5ml eppendorf tubes. Freeze these tubes in liquid nitrogen, then transfer them to -80℃ freezer.


Tansformation Protocol

  1. Take competent cell in an eppendorf tube from -80℃ freezer put in ice.
  2. Add 2ul plasmid to competent cell and place in ice for 5 minutes.
  3. Put the transformed cells into 42℃ water bath for 60 seconds.
  4. Then place the cells in ice for 2 minutes.
  5. Add 1ml LB to the cells and mixed.
  6. Put the eppendorf tube in 37℃ water bath and incubate for an hour.
  7. Spin down at 7000 rpm for 5 minutes and remove most of the supernatant.
  8. While the cells are incubated at 37℃ water bath spread 100ul Ampicilin(50mg/ml) on the plate. When the plate is dried, spread bacteria on the plate.
  9. Incubate at 37℃ incubater for 16~18 hours.


PCR

1. Dissolve the primers in water to have the concentration of 10nM.


2. PCR reaction mixer： 

 Template DNA（10ng/μl）		5
 10× PCR buffer			2
 10× dNTP（2mM）			2
 forward primer（10μM）		0.5
 reverse primer（10μM）		0.5
 Pfu DNA polymerase（2Kb）	0.1
 PCR water			9.9
 _______________________________________
 Total				20 μl


3. Put the reaction mixer in a PCR tube.

4.The PCR program is as follow :

4.1
94℃ 30 seconds
60℃ 30seconds
72℃ 2 minutes
Cycle 9 times


4.2
94℃ 30 seconds
55℃ 30seconds
72℃ 2 minutes
Cycle 34 times

Extend PCR product at 72℃ for 10 minutes


5. The PCR product was examed by electrophoresis in 1％ agarose.



T-A cloning

Take an eppendorf tube and add following component one by one and mix well,incubated at 4℃ overnight. 


 2x ligase buffer	7.5μl
 Insert(Aeq.-GFP)	5.5μl
 Vector(pGEM-T-easy)	1μl
 T4 DNA exp 3/12	1μl
 _________________________________
 total			15μl


Colony PCR(To verify the presence of our gene of interest)

  1. Take 10μl of bacterial culture, spin down at 14000 rpm for 10 min.
  2. Discard the supernatant
  3. Add 500μl ddH20, Vortex
  4. Boil for 20 min.
  5. Take 5μl of above bacterial lysate, and add 10x dNTP 2μl, 10x Buffer 2μl, forward primer（10μM）0.5μl reverse primer（10μM）0.5μl, Taq DNA polymerase 0.1μl, ddH20
  6. Use the PCR to amplify our product：PCR program 
 95℃ 4 min 
 94℃ 30seconds 
 55℃ 40seconds 
 72℃ 2 min
 Cycle 34 times
 25℃ 2 min

　　7. The PCR product was examed by electrophoresis in 1％ agarose.

Plasmid extraction(Homemade)

  1. Transfer 1.5ml of bacterial culture to each well(24 wells plate)
  2. pellet cells by centrifuging at 33000 rpm for 10min at 4℃
  3. carefully remove the supernatant
  4. add 100μl of Solution 1 (*)to each well, and vortex
  5. add 200μl of Solution 2 (*)to each well, and mix gently
  6. add 150μl of Solution 3 (*)to each well
  7. spin down 3000rpm at 4℃ for 10min
  8. add 1 ml 100% EtOH to new well
  9. Transfer the supernatant to the new well, containing 100% EtOH.
  10. spin down 3300rpm at 4℃ for 30min.
  11. carefully remove the supernatant.
  12. add 75% EtOH to wash pellets, then remove the supernantant, then air dry.
  13. add 40μl ddH2O to each well, to dissolve with plasmid DNA
  14. store the plate in 4℃ 
 (*)Sol 1: 10m Miris/0.5mM HEDTA, PH 7.4 buffer.
    Sol 2: 0.2N NaOH/1% SDS
    Sol 3: 3M KOAC/HOAC

Digestion

Digestion mixture 

 DNA        20μl
 10x buffer 3μl
 Enzyme     1μl
 RNase H2O  6μl
 __________________________
 Total      30μl

3. The order for adding materials to wells is from plenty to less 4. Place the plate in 37℃water bath overnight


Ligation

Take an eppendorf tube and add following component one by one and mix well,incubated at 16℃ overnight. 


 Insert(Aeq.-GFP)	7.5μl
 Vector(pSB1A3)  	5.5μl
 10X ligase buffer	1μl
 T4 DNA ligase   	1μl
 _________________________________
 total			30μl
Retrieved from "http://2009.igem.org/Team:TzuChiU_Formosa/Protocol"