Biomod/2013/BU/protocols

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<b>Gel Prep</b>:
<b>Gel Prep</b>:
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(For a 1% Agarose Gel) <br />
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For 1% Agarose Gel: <br />
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Weigh out 0.5g of Agarose on a scale. Pour the the agarose into a 250mL erlenmeyer flask. Pipette 5mL of 5X Agarose Gel Buffer into a 100mL graduated cylinder and dilute 10 fold to a total volume of 50mL. Pour diluted buffer into the agarose erlenmeyer flask and microwave until the solution begins to boil, stopping the microwave and swirling the contents of the flask every 15 seconds.</p>
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<UL>
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<LI>0.5g Agarose powder
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<LI>5mL 5X Agarose Gel Buffer
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<LI>45mL ddH<sub>2</sub>O
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</UL>
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Add 500ul of MgCl<sub>2</sub> and 5ul SybrSafe gel dye. Gently swirl the flask to mix contents and then pour the contents into a gel mold. Place the well comb in the mold and freeze for 20 minutes.
Add 500ul of MgCl<sub>2</sub> and 5ul SybrSafe gel dye. Gently swirl the flask to mix contents and then pour the contents into a gel mold. Place the well comb in the mold and freeze for 20 minutes.

Revision as of 15:40, 24 July 2013

Contents

Boston University

BIOMOD 2013 Design Competition

Protocols


Gel Electrophoresis

Gel Prep:

For 1% Agarose Gel:

  • 0.5g Agarose powder
  • 5mL 5X Agarose Gel Buffer
  • 45mL ddH2O


Add 500ul of MgCl2 and 5ul SybrSafe gel dye. Gently swirl the flask to mix contents and then pour the contents into a gel mold. Place the well comb in the mold and freeze for 20 minutes.

Gel Buffer

To prepare the buffer that fills the gel electrophoresis chamber, pour 30mL of the 5X buffer into a 500mL flask and dilute the total volume of the solution to 300mL. Set aside until the gel is solidified.

Sample Prep

Aliquot the desired volume of sample to be run in the gel, ensuring not to exceed the well capacity. Add loading dye and mix via pipetting.

Running the Gel

Place the gel in the electrophoresis chamber and fill the chamber with the gel buffer. Remove the comb and load the sample into the wells. Connect the electrodes and run the gel at the desired voltage for the desired length of time.

To prevent overheating of the gel, surround the gel electrophoresis chamber with ice.


TEM Prep

Select a TEM grid using specialized forceps and set the forceps with the grid down on a flat surface. Pipette 3uL of the desired sample onto the grid and let it sit for 2 minutes. Afterwards, wick away any excess moisture with filter paper. Next dip the TEM grid, sample side down, into a drop of uranyl acetate and hold for 30 seconds. Afterwards, wick away any excess moisture with filter paper. Lastly, dip the TEM grid, sample side down, into a drop of ddH2O and hold for 30 seconds. Afterwards wick away any excess moisture. Let the grid sit in the forceps on a flat surface for 1 minute until the surface of the grid is completely dry.


Measuring Concentrations via NanoDrop

Open the NanoDrop program and select Nucleic Acids. Blank the instrument with 2μL of the solution which the sample is suspended in. Wipe away any excess solution with a Kimwipe and then pipette 2μL of the sample onto the instrument and click "Measure." Repeat for as many samples as necessary. In between samples, rinse the instrument with 2μL ddH2O.


Purification via Dialysis Filters

During small scale experiments, 500μL 50kDa dialysis filters were used. The entire sample volume is pipetted into the filter and then the total volume is brought to 500μL with isolation buffer. The sample is spun in a centrifuge at 4000 RCF for 15 minutes. The staples are discarded and the volume of the filter is refilled to 500μL. The sample is spun again. This process is repeated for a maximum of 3 spins with a single filter. To retrieve the sample from the filter, the filter column is inverted and placed in a new tube. This tube is then spun at 2000 RF for 2 minutes.

Gel Purification

Run the samples in a 1.5% agarose gel until product band and misfolded band separate sufficiently. Cut the product band from the gel, leaving behind as much excess gel as possible. Transfer the gel band to a gel filtration tube and freeze the sample for 10 minutes. Spin the sample down for 14 minutes at 5000 RCF. Pipette out the recovered sample.
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