Difference between revisions of "Team:NYU Shanghai/Protocols"

Revision as of 12:34, 15 September 2015

Project
- Design
- Parts
- Code
- Judging
Team
Outreach
Notebook

Protocols

We built our constructs from digests and ligations of pre-made biobrick parts. Our general conclusion is that 3A assembly is generally inefficient, and an insufficient method for adding small parts (such as a terminator) to a larger construction within pSB1C3. We learned that ratios were extremely important in the process of 3A Assembly, and we made a summary sheet of the equations we used in pre-digest and pre-ligation that accounts for digest dilution and amount needed to ensure results are seen on a gel, not just ligation ratios.

Recipes

LB-Agar Plates

LB Broth

SOC Media

Making Color

Luciferase

Chromoproteins

3A Assembly

Transformation

Miniprep

Estimated time

Materials

Biomiga Miniprep Kit

Procedure

Harvest the bacterial culture by centrifugation for 1 min at 10,000 rpm. Pour off the supernatant and blot the inverted tube on a paper towel to remove residue medium. Remove the residue medium completely.
Add 250 µL Buffer A1 (Add RNase A to Buffer A1 before use) and completely resuspend bacterial pellet by vortexing or pipetting
Add 250 µL Buffer B1, mix gently by inverting the tube 10 times (do not vortex), and incubate at room temperature for 5 minutes.
Add 350 µL Buffer N1, mix completely by inverting/shaking the vial for 5 times and sharp hand shaking for 2 times.
Note: Incubating the lysate in ice for 1 min will improve the yield.
Centrifuge the lysate at 13,000 rpm for 10 minutes at room temperature. If the lysate doesn’t appear clean, reverse the tube angle, centrifuge for 5 more minutes and then transfer the clear lysate to DNA column.
Carefully transfer the clear lysate into a DNA column with a collection tube, avoid the precipitations, spin at 13,000 rpm for 1 minute, discard the flow-through and put the column back to the collection tube.
Add 500 µL Buffer KB into the spin column, centrifuge at 13,000 rpm for 1 minute. Remove the spin column from the tube and discard the flow-through. Put the column back to the collection tube.
Add 650 µL DNA Wash Buffer (Add ethanol to DNA wash buffer before use) into the spin column, centrifuge at 13,000 rpm for 1 minute at room temperature. Remove the spin column from the tube and discard the flowthrough.
Reinsert the spin column, with the lid open, into the collection tube and centrifuge for 2 minutes at 13,000 rpm.
Carefully transfer the spin column into a sterile 1.5 mL tube and add 50-100 µL (> 50 µL) Sterile ddH20 or Elution Buffer into the center of the column and let it stand for 2 minutes. Elute the DNA by centrifugation at 13,000 rpm for 1 minute. Reload the eluate into the column and elute again.

Restriction Digest

Ligation

Gel Electrophoresis

Gel Extraction

Estimated time:

Materials
MinElute Midi Gel Extraction Kit

Procedure

Pre-weigh a 2.0mL microcentrifuge tube
Excise DNA fragment from agarose gel with clean, sharp scalpel. Place in the pre-weighed microcentrifuge tube. Minimize the exposure of the DNA samples under UV and amount of gel cut with DNA.
Weigh the tube and calculate the weight of the gel. For every 1 volume of gel (100mg = 100µl) add 3 times the volume of Buffer QG. The maximum amount of gel slice per spin column is 400mg.For >2% agarose gels, add 6 volumes of Buffer QG.
Incubate at 50ºC for 10 minutes (or until the gel has completely dissolved). Vortex the tube every 2-3 minutes during incubation to help dissolve the gel. If color is orange or violet after gel slice has dissolved, add 10µl 3M sodium acetate, pH 5.0. The color of the mixture will turn to yellow.
Add 1 gel volume of isopropanol to the sample and mix by inverting.
Place a MinElute spin column in a provided 2mL collection tube. Apply the sample in the 2.0mL microcentrifuge tube to the MinElute column and centrifuge for 1 min at 13,000 rpm. Discard the flow-through and place the MinElute column back into the same collection tube. If the sample volume exceeds 800µl, simply reload and spin again.
Add 500µl Buffer QG to the MinElute column and centrifuge for 1 minute at 13,000 rpm. Discard flow-through and place the MinElute column back into the same collection tube.
Add 750µl Buffer PE to MinElute column and centrifuge for 1 minute at 13,000 rpm. Discard flow-through and place the MinElute column back into the same collection tube. If the DNA will be used for salt-sensitive applications, such as direct sequencing and blunt-ended ligation, let the column stand 2-5 minute after addition of Buffer PE.
Centrifuge the column in the 2mL collection tube for 1 minute at 13,000 rpm again to remove residual ethanol.
Place each MinElute column into a clean 1.5mL microcentrifuge tube. To elute DNA, add 10µl Buffer EB or water to the center of the MinElute membrane. Let the column stand for 1 minute, and centrifuge the column for 1 minute at 13,000rpm.
Repeat step 12 but this time load the flow-through back to the membrane. Let the column stand for 1 minute, and centrifuge the column for 1 minute at 13,000rpm.
Check Gel extraction product with Nanodrop

PCR

PCR Cleanup

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@@ Line 209: / Line 209: @@
 <div id="overview">
    <h3>Protocols</h3>
+ <h6>We built our constructs from digests and ligations of pre-made biobrick parts. Our general conclusion is that 3A assembly is generally inefficient, and an insufficient method for adding small parts (such as a terminator) to a larger construction within pSB1C3. We learned that ratios were extremely important in the process of 3A Assembly, and we made a summary sheet of the equations we used in pre-digest and pre-ligation that accounts for digest dilution and amount needed to ensure results are seen on a gel, not just ligation ratios. </h6>
 </div>
@@ Line 291: / Line 292: @@
 <div id="assembly" class="column">
    <h4>3A Assembly</h4>
- <h6>We built our constructs from digests and ligations of pre-made biobrick parts. Our general conclusion is that 3A assembly is generally inefficient, and an insufficient method for adding small parts (such as a terminator) to a larger construction within pSB1C3. We learned that ratios were extremely important in the process of 3A Assembly, and we made a summary sheet of the equations we used in pre-digest and pre-ligation that accounts for digest dilution and amount needed to ensure results are seen on a gel, not just ligation ratios. </h6>
 <div id="transform" class="collapsed" onclick="expandtransform()">
   <h5 style="display:inline-block"><span class="noselect">Transformation</span></h5>

Difference between revisions of "Team:NYU Shanghai/Protocols"

Revision as of 12:34, 15 September 2015

Project

Team

Outreach

Notebook

Protocols

Recipes

LB-Agar Plates

LB Broth

SOC Media

Making Color

Luciferase

Chromoproteins

3A Assembly

Transformation

Miniprep

Restriction Digest

Ligation

Gel Electrophoresis

Gel Extraction

PCR

PCR Cleanup