Team:Bielefeld-CeBiTec/Notebook/Protocols

From 2014.igem.org

(Difference between revisions)
Line 310: Line 310:
       </div>
       </div>
       <div class="content">
       <div class="content">
-
         <ul style="margin-left:30%; margin-right:30%" type="disc">
+
         <ul style="margin-left:10%; margin-right:10%" type="disc">
           <li> Dissolving the Gel Slice </li>  
           <li> Dissolving the Gel Slice </li>  
-
           <ul> <li> Following electrophoresis, excise DNA band from gel and place gel slice in a 1.5 mL microcentrifuge
+
           <ul> <li> Following electrophoresis, excise DNA band from gel and place gel slice in a 1.5 mL  
-
                     tube. </li>
+
                     microcentrifuge tube. </li>
-
               <li> Add 10 µL Membrane Binding Solution per 10 mg of gel slice. Vortex and incubate at 50-65°C until gel
+
               <li> Add 10 µL Membrane Binding Solution per 10 mg of gel slice. Vortex and incubate at 50-65°C until
-
                     slice is completely dissolved. </li> </ul>
+
                     gel slice is completely dissolved. </li> </ul>
           <li> Processing PCR Amplifications </li>
           <li> Processing PCR Amplifications </li>
           <ul> <li> Add an equal volume of Membrane Binding Solution to the PCR amplification. </li> </ul> <br>
           <ul> <li> Add an equal volume of Membrane Binding Solution to the PCR amplification. </li> </ul> <br>
Line 321: Line 321:
           <li> Binding of DNA </li>  
           <li> Binding of DNA </li>  
           <ul> <li> Insert SV Minicolumn into Collection Tube. </li>  
           <ul> <li> Insert SV Minicolumn into Collection Tube. </li>  
-
               <li> Transfer dissolved gel mixture or prepared PCR product to the Minicolumn assembly. Incubate at room
+
               <li> Transfer dissolved gel mixture or prepared PCR product to the Minicolumn assembly. Incubate at
-
                     temperature for 1 minute. </li>
+
                     room temperature for 1 minute. </li>
-
               <li> Centrifuge at 16,000 x g for 1 minute. Discard flowthrough and reinsert Minicolumn into Collection
+
               <li> Centrifuge at 16,000 x g for 1 minute. Discard flowthrough and reinsert Minicolumn into  
-
                     Tube. </li> </ul> <br>
+
                     Collection Tube. </li> </ul> <br>
           <li> Washing </li>  
           <li> Washing </li>  
           <ul> <li> Add 700 µL Membrane Wash Solution (ethanol added). Centrifuge at 16,000 x g for 1 minute. Discard
           <ul> <li> Add 700 µL Membrane Wash Solution (ethanol added). Centrifuge at 16,000 x g for 1 minute. Discard
                     flowthrough and reinsert Minicolumn into Collection Tube. </li>  
                     flowthrough and reinsert Minicolumn into Collection Tube. </li>  
-
               <li> Repeat Step before with 500 µL Membrane Wash Solution. Centrifuge at 16,000 x g for 5 minutes. </li>  
+
               <li> Repeat Step before with 500 µL Membrane Wash Solution. Centrifuge at 16,000 x g for 5 minutes.
-
               <li> Empty the Collection Tube and recentrifuge the column assembly for 1 minute with the microcentrifuge
+
              </li>  
-
                     lid open (or off) to allow evaporation of any residual ethanol. </li> </ul>
+
               <li> Empty the Collection Tube and recentrifuge the column assembly for 1 minute with the
 +
                     microcentrifuge lid open (or off) to allow evaporation of any residual ethanol. </li> </ul>
           <li> Elution </li>  
           <li> Elution </li>  
Line 357: Line 358:
           <li> Note: </li>  
           <li> Note: </li>  
           <ul> <li> All purification steps should be carried out at room temperature. </li>  
           <ul> <li> All purification steps should be carried out at room temperature. </li>  
-
               <li> All centrifugation should be carried out in a table-top microcentrifuge at >12000 x g(10 000-14 000
+
               <li> All centrifugation should be carried out in a table-top microcentrifuge at >12000 x g(10 000-14
-
                     rpm, depending on the rotor type). </li> </ul> <br>
+
                     000 rpm, depending on the rotor type). </li> </ul> <br>
           <li> Resuspend the pelleted cells in 250 µL of the Resuspension Solution. Transfer the cell suspension to a  
           <li> Resuspend the pelleted cells in 250 µL of the Resuspension Solution. Transfer the cell suspension to a  
-
               microcentrifuge tube. The bacteria should be resuspended completely by vortexing or pipetting up and down
+
               microcentrifuge tube. The bacteria should be resuspended completely by vortexing or pipetting up and
-
               until no cell clumps remain. </li>
+
               down until no cell clumps remain. </li>
           <ul> <li> <u>Note</u> Ensure RNase A has been added to the Resuspension Solution. </li> </ul>  
           <ul> <li> <u>Note</u> Ensure RNase A has been added to the Resuspension Solution. </li> </ul>  
           <li> Add 250 µL of the Lysis Solution and mix thoroughly by inverting the tube 4-6 times until the solution  
           <li> Add 250 µL of the Lysis Solution and mix thoroughly by inverting the tube 4-6 times until the solution  
Line 371: Line 372:
               times. </li>  
               times. </li>  
           <ul> <li> <u>Note</u> It is important to mix thoroughly and gently after the addition of the Neutralization
           <ul> <li> <u>Note</u> It is important to mix thoroughly and gently after the addition of the Neutralization
-
                     Solution to avoid localized  precipitation of bacterial cell debris. The neutralized bacterial lysate
+
                     Solution to avoid localized  precipitation of bacterial cell debris. The neutralized bacterial  
-
                     should become cloudly. </li> </ul>  
+
                     lysate should become cloudly. </li> </ul>  
           <li> Centrifuge for 5 minutes to pellet cell debris and chromosomal DNA. </li>  
           <li> Centrifuge for 5 minutes to pellet cell debris and chromosomal DNA. </li>  
-
           <li> Transfer the supernatant to the supplied GeneJET spin coloumn by decanting or pipetting. Avoid disburbing
+
           <li> Transfer the supernatant to the supplied GeneJET spin coloumn by decanting or pipetting. Avoid  
-
               or transferring the white  precipitate. </li>
+
               disburbing or transferring the white  precipitate. </li>
-
           <li> Centrifuge for 1 minute. Discard the flow-through and place the coloumn back into the same collection tube.
+
           <li> Centrifuge for 1 minute. Discard the flow-through and place the coloumn back into the same collection
-
          </li>  
+
              tube. </li>  
           <ul> <li> <u>Note</u> Do not add bleach to the flow-through. </li> </ul>  
           <ul> <li> <u>Note</u> Do not add bleach to the flow-through. </li> </ul>  
           <li> Add 500 µL of the Wash Solution (diluted with ethanol prior to first use) to the GeneJET spin column.  
           <li> Add 500 µL of the Wash Solution (diluted with ethanol prior to first use) to the GeneJET spin column.  
-
               Centrifuge for 30-60 seconds and discard the flow-through. Place the column back into the same collection
+
               Centrifuge for 30-60 seconds and discard the flow-through. Place the column back into the same  
-
               tube. </li>  
+
               collection tube. </li>  
           <li> Repeat the wash procedure (step before) using 500 µL of the Wash Solution. </li>
           <li> Repeat the wash procedure (step before) using 500 µL of the Wash Solution. </li>
-
           <li> Discard the flow-through and centrifuge for an additional  1 minute to remove residual Wash Solution. This
+
           <li> Discard the flow-through and centrifuge for an additional  1 minute to remove residual Wash Solution.
-
               step is essential to avoid residual ethanol in plasmid preps. </li>
+
               This step is essential to avoid residual ethanol in plasmid preps. </li>
-
           <li> Transfer the GeneJET spin column into a fresh 1.5 mL microcentrifuge tube (not included).  Add 50 µL of the
+
           <li> Transfer the GeneJET spin column into a fresh 1.5 mL microcentrifuge tube (not included).  Add 50 µL of
-
               Elution Buffer to the center of GeneJET spin column membrane to elute the plasmide DNA. Take care not to
+
               the Elution Buffer to the center of GeneJET spin column membrane to elute the plasmide DNA. Take care
-
               contact the membrane with the pipette tip. Incubate for 2 minutes at room temperature and centrifuge for 2  
+
               not to contact the membrane with the pipette tip. Incubate for 2 minutes at room temperature and  
-
              minutes. </li>  
+
              centrifuge for 2 minutes. </li>  
-
           <ul> <li> <u>Note</u> An additional elution step (optional) with Elution Buffer or water will recover residual
+
           <ul> <li> <u>Note</u> An additional elution step (optional) with Elution Buffer or water will recover  
-
                     DNA from the membrane and increase the overall yield by 10-20%. For elution of plasmids or cosmids >20
+
                     residual DNA from the membrane and increase the overall yield by 10-20%. For elution of plasmids
-
                    kb, prewarm Elution Buffer to 70°C before applying to silica membrane. </ul> </li>
+
                    or cosmids >20 kb, prewarm Elution Buffer to 70°C before applying to silica membrane. </ul> </li>
           <li> Discard the column and store the purified plasmid DNA at -20°C.</li>
           <li> Discard the column and store the purified plasmid DNA at -20°C.</li>
       </div>
       </div>

Revision as of 20:28, 11 August 2014




Protocols

LB medium

LB medium

  • 10 g Trypton
  • 5 g yeast extract
  • 10 g NaCl
  • 12 g Agar-Agar (for plates)
  • Adjust pH to 7.4
TAE buffer

TAE buffer

  • 1 L of 50x TAE buffer
  • 242.48 g Tris
  • 41.02 g sodium acetate
  • 18.612 g EDTA
  • Adjust pH to 7.8 with acetic acid
  • Solve in dH2O
  • Dilute 20 mL 50x stock in 1L dH2O for 1x Buffer for PAGE
M9 medium

M9 medium

  • To prepare 1 liter of M9 minimal medium add the following components to 836.7 mL sterile distilled water.
    To avoid precipitation, start with CaCl2 and mix the solution thoroughly after addition of a component.
  • 100 mL 10 X M9 salt solution
  • 50 mL 20 X carbon source
  • 10 mL 100 X trace element solution
  • 1 mL autoclaved 1 M MgSO4
  • 0.3 mL autoclaved 1 M CaCl2
  • 1 mL filter sterilized 1 g/L biotin
  • 1 mL filter sterilized 1 g/L thiamin
M9 salt stock solution

M9 salt stock solution

  • 75.2 g Na2HPO4 x 2H2O
  • 30 g KH2PO4
  • 5 g NaCl
  • 5 g NH4Cl
  • Dissolve the salts in 800 mL water and adjust the pH to 7.2 with NaOH. Add water to a final volume of 1 L and autoclave for 15 minutes at 121 °C.
Colony PCR

Colony PCR

  • Pick one colony with a sterile tip and elute it in 100 µL ddH20 or medium
  • Store the colony in 4 °C while colony PCR is running
  • One reaction mix contains:
    • 10 µL 5x buffer
    • 2 µL MgCl2 (25 mM stock)
    • 1 µL dNTPs
    • 0.5 µL primer mix (prefix/suffix primers or sequencing primers)
    • 35.25 µL ddH2O
    • 0.25 µL GoTaq polymerase (Promega)
    • 1 µL template
  • PCR program:
    • Start: 3 min, 98 °C
    • 30 cycles of:
      • 30 s, 98 °C
      • 30 s, 55 °C
      • 30 s / 1 kb template, 72 °C
    • Finish: 5 min, 72 °C
  • Gel electrophoresis: check the fragment size
  • Plate the correct colony
Generating electrocompetent cells

Generating electrocompetent cells
  • Material:
    • 550 mL LB-Medium
    • 1 L cooled bidest. H2O
    • 150 mL cooled 10 % glycerine
    • 10 pre-cooled 50 mL Falcons
  • Protocol:
    • Inoculate 2x3 mL LB with bacterial stock; incubate over night at 37 °C and 200 rpm
    • Inoculate 2x250 mL LB with the over night cultures in 1-litre-flask at 37 °C and 140 rpm
    • Incubate until OD600 0,4-0,6
    • Cool the culture 15-30 minutes on ice
    • Onwards all steps at 4°C
    • Divide the cultures into cooled 50 mL Falcons and centrifugate at 4000 rpm, 4 °C for 15 minutes, make sure to slowly accelerate and deccelerate
    • Discard supernatant
    • Resuspend pellet in 5 mL cooled bidest H2O (and don't get frustrated while doing it, keep shaking gently)
    • Pool two suspensions each, add bidest H2O up to 50 mL and centrifugate again (see centrifugation above)
    • Discard supernatant
    • Resuspend pellet in 5 mL cooled bidest H2O
    • Add bidest H2O up to 50 mL and centrifugate again (see centrifugation above)
    • Discard supernatant
    • Resuspend pellet in 5 mL cooled 10 % glycerine
    • Transfer suspensions in two 50 mL Falcons and centrifugate again (see centrifugation above)
    • Discard supernatant
    • Add volume of 10 % glycerine that is approximately equal to the volume of the pellet and resuspend
    • Divide cells in 50 µL aliquots and freeze in liquid N2 immediately
    • Store at -80 °C
Transformation via electroporation

Transformation via electroporation

  • Thaw 50 µL competent E.coli cells on ice, dilute with icecold 50 µL glycerine (10 %) if necessary
  • Add 0.5-5 µL plasmid to 50 µl electrocompetent cells
  • Store cells on ice for 1 minute
  • Electroporate at U = 2.5 kV, C = 25 µF, R = 400 ?
  • Transfer transformation reaction to 450 µL SOC-Medium and shake 1 h at 37 °C
  • Centrifuge 2 min at 2000 rpm and plate on selective LB-Medium
  • Incubate over night at 37 °C
SOC-medium

SOC-medium

  • Add the following components for 900 ml of distilled H2O:
    • 20 g Trypton
    • 5 g Bacto Yeast Extract
    • 2 mL of 5 M NaCl
    • 2.5 ml of 1 M KCl
    • 10 ml of 1 M MgCl2
    • 10 ml of 1 M MgSO4
    • 20 ml of 1 M glucose
50X TAE Stock Solution

50X TAE Stock Solution

  • For each litre of solution:
    • 242 g Tris Base (MW=121.1)
    • 57.1 mL Glacial Acetic Acid
    • 100 mL 0.5 M EDTA

  • mix Tris with stir bar to dissolve in about 600 mL of ddH2O.
  • add the EDTA and Acetic Acid.
  • bring final volume to 1 L with ddH20.
  • store at room temperature.

  • Note: Final (1x) working concentration:
    • 0.04 M Tris - Acetate
    • 0.001 M EDTA
50X Modified TAE Stock Solution

50X Modified TAE Stock Solution

  • For each litre of solution:
    • 242 g Tris Base (MW=121.1)
    • 57.1 mL Glacial Acetic Acid
    • 10 mL 0.5 M EDTA

  • mix Tris with stir bar to dissolve in about 600 mL of ddH2O.
  • add the EDTA and Acetic Acid, pH to 8.0.
  • bring final volume to 1 L with ddH2O.
  • store at room temperature.

  • Note: Final (1x) working concentration:
    • 0.04 M Tris - Acetate
    • 0.0001 M EDTA
DNA Purification by Centrifugation

DNA Purification by Centrifugation

  • Dissolving the Gel Slice
    • Following electrophoresis, excise DNA band from gel and place gel slice in a 1.5 mL microcentrifuge tube.
    • Add 10 µL Membrane Binding Solution per 10 mg of gel slice. Vortex and incubate at 50-65°C until gel slice is completely dissolved.
  • Processing PCR Amplifications
    • Add an equal volume of Membrane Binding Solution to the PCR amplification.

  • Binding of DNA
    • Insert SV Minicolumn into Collection Tube.
    • Transfer dissolved gel mixture or prepared PCR product to the Minicolumn assembly. Incubate at room temperature for 1 minute.
    • Centrifuge at 16,000 x g for 1 minute. Discard flowthrough and reinsert Minicolumn into Collection Tube.

  • Washing
    • Add 700 µL Membrane Wash Solution (ethanol added). Centrifuge at 16,000 x g for 1 minute. Discard flowthrough and reinsert Minicolumn into Collection Tube.
    • Repeat Step before with 500 µL Membrane Wash Solution. Centrifuge at 16,000 x g for 5 minutes.
    • Empty the Collection Tube and recentrifuge the column assembly for 1 minute with the microcentrifuge lid open (or off) to allow evaporation of any residual ethanol.
  • Elution
    • Carefully transfer Minicolumn to a clean 1.5 mL microcentrifuge tube.
    • Add 15 µL of Nuclease-Free Water to the Minicolumn. Incubate at 60°C for 5 minutes. Centrifuge at 16,000 x g for 1 minute. Repeat this step.
    • Discard Minicolumn and store DNA at 4°C or -20°C.
Purification Protocol

Puricfication Protocol

  • Note:
    • All purification steps should be carried out at room temperature.
    • All centrifugation should be carried out in a table-top microcentrifuge at >12000 x g(10 000-14 000 rpm, depending on the rotor type).

  • Resuspend the pelleted cells in 250 µL of the Resuspension Solution. Transfer the cell suspension to a microcentrifuge tube. The bacteria should be resuspended completely by vortexing or pipetting up and down until no cell clumps remain.
    • Note Ensure RNase A has been added to the Resuspension Solution.
  • Add 250 µL of the Lysis Solution and mix thoroughly by inverting the tube 4-6 times until the solution becomes viscous and slightly clear.
    • Note Do not vortex to avoid shearing of chromosomal DNA. Do not incubate for more than 5 minutes to avoid denaturation of supercoiled plasmid DNA.
  • Add 350 µL of the Neutralization Solution and mix immediately and thoroughly by inverting the tube 4-6 times.
    • Note It is important to mix thoroughly and gently after the addition of the Neutralization Solution to avoid localized precipitation of bacterial cell debris. The neutralized bacterial lysate should become cloudly.
  • Centrifuge for 5 minutes to pellet cell debris and chromosomal DNA.
  • Transfer the supernatant to the supplied GeneJET spin coloumn by decanting or pipetting. Avoid disburbing or transferring the white precipitate.
  • Centrifuge for 1 minute. Discard the flow-through and place the coloumn back into the same collection tube.
    • Note Do not add bleach to the flow-through.
  • Add 500 µL of the Wash Solution (diluted with ethanol prior to first use) to the GeneJET spin column. Centrifuge for 30-60 seconds and discard the flow-through. Place the column back into the same collection tube.
  • Repeat the wash procedure (step before) using 500 µL of the Wash Solution.
  • Discard the flow-through and centrifuge for an additional 1 minute to remove residual Wash Solution. This step is essential to avoid residual ethanol in plasmid preps.
  • Transfer the GeneJET spin column into a fresh 1.5 mL microcentrifuge tube (not included). Add 50 µL of the Elution Buffer to the center of GeneJET spin column membrane to elute the plasmide DNA. Take care not to contact the membrane with the pipette tip. Incubate for 2 minutes at room temperature and centrifuge for 2 minutes.
    • Note An additional elution step (optional) with Elution Buffer or water will recover residual DNA from the membrane and increase the overall yield by 10-20%. For elution of plasmids or cosmids >20 kb, prewarm Elution Buffer to 70°C before applying to silica membrane.
  • Discard the column and store the purified plasmid DNA at -20°C.

Retrieved from "http://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols"