Difference between revisions of "Team:Arizona State/Experiments"

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</ol>  
 
</ol>  
 
</div>
 
</div>
 +
<div class="container">
 +
 +
<h3>[2A] DNA Restriction Digest</h3>
 +
<ol>
 +
<li>Gather DNA sample, digestion buffer, and restriction enzymes from cold storage</li>
 +
<li>Label tubes</li>
 +
<li>Create the below reaction mixture </li>
 +
<li>Place mixture in 37°C heat block for 10 minutes</li>
 +
</ol>
 +
 +
<table style="width:100%">
 +
  <tr>
 +
    <th>Component</th>
 +
    <th>Volume for 25uL reaction</th>
 +
  </tr>
 +
  <tr>
 +
    <td>DNA Sample</td>
 +
    <td>15uL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>10x FastDigest Digestion Buffer</td>
 +
    <td>2.5uL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Restriction Enzyme 1</td>
 +
    <td>1uL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Restriction Enzyme 2</td>
 +
    <td>1uL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>DI H2O</td>
 +
    <td>5.5uL</td>
 +
  </tr>
 +
</table>
 +
</div>
 +
<h3>[2B] Gel Verification/Extraction</h3>
 +
<ol>
 +
<li>Make 1% gel by adding .6g of agarose to 60mL of 1x TAE buffer</li>
 +
<li>Swirl in glass flask and microwave for 40s</li>
 +
<li>Remove from microwave and swirl again. Microwave again for 40s</li>
 +
<li>Let cool until safe to touch. Add 6uL of SYBR safe red stain</li>
 +
<li>Pour mixture into gel mold with comb set up</li>
 +
<li>Fill gel electrophoresis apparatus with 1x TAE </li>
 +
<li>Remove comb from gel and submerge gel in apparatus</li>
 +
<li>Add 4uL of 1kb+ blue ladder to the first well</li>
 +
<li>Add samples mixed with loading dye to other wells</li>
 +
<li>Connect negative/positive ends to apparatus. Run at 110V</li>
 +
<li>Run for 30min-1hr. Remove and take to UV imager</li>
 +
<li>Photograph under UV light. If doing gel extraction, use scalpel to cut out blocks of gel containing desired bands</li>
 +
<li>Gel purify using Qiagen Gel Purification kit</li>
 +
<li>(If extracting)Use Nanodrop Spectrophotometer to measure DNA concentration</li>
 +
</ol>
 +
 +
<table style="width:100%">
 +
  <tr>
 +
    <th>Component</th>
 +
    <th>Volume for 25uL reaction</th>
 +
  </tr>
 +
  <tr>
 +
    <td>DNA Sample</td>
 +
    <td>15uL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>10x FastDigest Digestion Buffer</td>
 +
    <td>2.5uL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Restriction Enzyme 1</td>
 +
    <td>1uL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Restriction Enzyme 2</td>
 +
    <td>1uL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>DI H2O</td>
 +
    <td>5.5uL</td>
 +
  </tr>
 +
</table>
 
<p>
 
<p>
 
<h5>What should this page contain?</h5>
 
<h5>What should this page contain?</h5>

Revision as of 00:34, 5 September 2016

Protocols

[1A] Polymerase Chain Reaction

PCR is used to rapidly amplify certain segments of DNA that are selected via designed primers. This protocol was used to accomplish a variety of goals, from extraction of parts from a cloning vector to the addition of restriction cut sites at the ends of parts.

  1. Defrost template, 2x Master Mix and primers
  2. Determine desired total working volume (~25uL)
  3. Label reaction tubes
  4. Create below reaction mix
  5. Place mixture in thermal cycler at settings shown below
Part Concentration Volume for 25uL reaction
2x Master Mix 2x 12.5uL
dsDNA Template - 1uL
Forward primer - 1uL
Reverse primer - 1uL
DI H2O - 9.5uL

Sample Reaction

This is an example protocol used in the thermal cycler, durations and temperatures subject to change

Step Name # of Cycles Temperature(℃) Duration(min)
Initial 1 98 3
Denaturation 30 98 0.5
Annealing 30 56 0.5
Elongation 30 72 0.5
Final Elongation 1 72 10
Storage 1 4 ∞

[1B] PCR Cleanup

The Qiagen Qiaquick PCR cleanup kit was used to purify the thermal cycler product and remove remaining polymerases and nucleotides.

  1. Gather the solutions from the PCR cleanup kit
  2. Mix 5 times volume of Buffer PB with PCR reaction tube
  3. Add 10uL 3M sodium acetate
  4. Spin down the mixture in a QIAquick filter column at max speed for 60s. Discard flow-through and replace column into tube
  5. Add 750uL of Buffer PE to the mixture and spin down at max speed for 60s to wash. Discard flow-through and replace column
  6. Centrifuge the tube one more time to remove any remaining wash buffer
  7. Place column in clean 1.5mL plastic tube
  8. Add 30uL of Buffer EB to the column and let stand for 1min. Centrifuge at max speed for 1 min.

[2A] DNA Restriction Digest

  1. Gather DNA sample, digestion buffer, and restriction enzymes from cold storage
  2. Label tubes
  3. Create the below reaction mixture
  4. Place mixture in 37°C heat block for 10 minutes
Component Volume for 25uL reaction
DNA Sample 15uL
10x FastDigest Digestion Buffer 2.5uL
Restriction Enzyme 1 1uL
Restriction Enzyme 2 1uL
DI H2O 5.5uL

[2B] Gel Verification/Extraction

  1. Make 1% gel by adding .6g of agarose to 60mL of 1x TAE buffer
  2. Swirl in glass flask and microwave for 40s
  3. Remove from microwave and swirl again. Microwave again for 40s
  4. Let cool until safe to touch. Add 6uL of SYBR safe red stain
  5. Pour mixture into gel mold with comb set up
  6. Fill gel electrophoresis apparatus with 1x TAE
  7. Remove comb from gel and submerge gel in apparatus
  8. Add 4uL of 1kb+ blue ladder to the first well
  9. Add samples mixed with loading dye to other wells
  10. Connect negative/positive ends to apparatus. Run at 110V
  11. Run for 30min-1hr. Remove and take to UV imager
  12. Photograph under UV light. If doing gel extraction, use scalpel to cut out blocks of gel containing desired bands
  13. Gel purify using Qiagen Gel Purification kit
  14. (If extracting)Use Nanodrop Spectrophotometer to measure DNA concentration
Component Volume for 25uL reaction
DNA Sample 15uL
10x FastDigest Digestion Buffer 2.5uL
Restriction Enzyme 1 1uL
Restriction Enzyme 2 1uL
DI H2O 5.5uL

What should this page contain?
  • Protocols
  • Experiments
  • Documentation of the development of your project
Inspiration

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