20.109(S13):DNA extraction (Day2)

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(Part 1: DNA extraction from bird stool, initiate)
(Part 1: DNA extraction from bird stool, initiate)
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===Part 1: DNA extraction from bird stool, initiate===
===Part 1: DNA extraction from bird stool, initiate===
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<font color=red>Note about increasing times for those with centrifuges that reach only 16K instead of 20K. And about 2 mL vs. 1.5 mL tube, not to mix up.</font color>
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The following protocol requires many tube changes. Be sure that each tube is clearly labeled with your sample number to avoid swapping samples with your partner.
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Before beginning this protocol, check the maximum spin speed of your centrifuge. Some centrifuges reach 20,000 g and others reach only 16,000 g, and the time for centrifugation will have to be adjusted proportionally. Note that ''rpm'' stands for rotations per minute while ''rcf'' stands for "relative centrifugal force." It is ''rcf'' that is equivalent to g-force, not ''rpm'', because different sized rotors will impart different forces at the same rotational speed.
#Obtain your 100 &mu;L bird stool sample from the teaching bench ice bucket, according to the number you are assigned on today's Talk page.  
#Obtain your 100 &mu;L bird stool sample from the teaching bench ice bucket, according to the number you are assigned on today's Talk page.  
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#*<font color=red>One per person or per pair??</font color>
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#*Work quickly and keep the sample on your ice bucket until you have finished adding the lysis reagent.
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#*Work quickly to avoid thawing the frozen samples and keep on ice when not in use.
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#Immediately add 1.4 mL of the lysis reagent (called buffer ASL) and vortex for ~ 1 min, until the solution is homogeneous.
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#Immediately add 1.4 mL of buffer ASL and vortex for ~ 1 min, until the solution is homogeneous.
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#*The fastest way to add the appropriate amount of ASL is to add 0.7 mL twice; that way you don't have to rotate the pipet setting in between additions.
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#*A few insoluble particulates may remain. Stop vortexing when the sample no longer visibly changes over a 20 sec interval.
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#*A few insoluble particulates may remain. Try vortexing for another 20-30 sec interval up to four more times, and stop vortexing when the sample no longer visibly changes over that interval.
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#Heat at either 70 &deg;C for 5 min, using the heat block at the front bench.
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#Heat at 70 &deg;C for 5 min on the heat block at the front bench.
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#Vortex for 15 sec and centrifuge for 1 min at 20,000 rcf.
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#Vortex for 15 sec and centrifuge for 1 min at 20,000 rcf or 1.5 min at 16,000 rcf. Place your tubes so that weight is equally distributed in the centrifuge.
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#Transfer 1.2 mL of supernatant into a fresh 2 mL tube.
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#*Unfortunately, your centrifuges cannot be set for 1.25 min exactly.
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#Transfer 1.2 mL of supernatant into a fresh '''2 mL tube'''.
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#*Be sure to use the special 2 mL eppendorfs here and not the standard 1.5 mL eppendorf tubes.
#Hold the foil-covered InhibitEX tablet over the tube, and gently push until the tablet pierces through the foil and falls into the tube.
#Hold the foil-covered InhibitEX tablet over the tube, and gently push until the tablet pierces through the foil and falls into the tube.
#Vortex until completely dissolved, which takes about 3 min for these samples.  
#Vortex until completely dissolved, which takes about 3 min for these samples.  
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#Incubate 1 min longer (with no shaking), and then centrifuge for 3 min.
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#*The solution will be homogeneous but somewhat thick.
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#Transfer the supernatant <font color=red>(usually about X mL)</font color> to a 1.5 mL tube and again centrifuge 3 min.
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#Incubate 1 min longer on a tube stand (with no shaking), and then centrifuge for 3 min (20K g) or 4 min (16K g).
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#In a fresh 1.5 mL tube, dispense 15 &mu;L proteinase K. Only then should you add 200 &mu;L of the supernatant above and 200 &mu;L buffer AL, pipetting to mix each time. Finally, add 10 &mu;L chitinase.
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#Transfer the supernatant <font color=red>(usually about X mL)</font color> to a '''1.5 mL tube''' and again centrifuge 3 or 4 min as needed.
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#Vortex for 15 sec (until solution is homogeneous) and incubate at 56 &deg;C for about 2 hours <font color=red>[1.5??]</font color>.
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#In a fresh '''1.5 mL tube''', dispense 15 &mu;L proteinase K. Only then should you add 200 &mu;L of the supernatant above followed by 200 &mu;L of buffer AL, pipetting to mix each time. Finally, add 10 &mu;L chitinase.
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#Vortex for 15 sec (until solution is homogeneous) and incubate in the 56 &deg;C oven for about 2 hours <font color=red>[1.5??]</font color>.
===Part 2: Writing Across the Curriculum session===
===Part 2: Writing Across the Curriculum session===

Revision as of 16:36, 5 January 2013

20.109(S13): Laboratory Fundamentals of Biological Engineering

Home        Schedule Spring 2013        Assignments       
DNA Engineering        Protein Engineering        Cell Engineering              

Contents

Introduction

background on DNA extraction

background about sample choices -- bird species, time of year, cloacal vs stool maybe?

Protocols

Part 1: DNA extraction from bird stool, initiate

The following protocol requires many tube changes. Be sure that each tube is clearly labeled with your sample number to avoid swapping samples with your partner.

Before beginning this protocol, check the maximum spin speed of your centrifuge. Some centrifuges reach 20,000 g and others reach only 16,000 g, and the time for centrifugation will have to be adjusted proportionally. Note that rpm stands for rotations per minute while rcf stands for "relative centrifugal force." It is rcf that is equivalent to g-force, not rpm, because different sized rotors will impart different forces at the same rotational speed.

  1. Obtain your 100 μL bird stool sample from the teaching bench ice bucket, according to the number you are assigned on today's Talk page.
    • Work quickly and keep the sample on your ice bucket until you have finished adding the lysis reagent.
  2. Immediately add 1.4 mL of the lysis reagent (called buffer ASL) and vortex for ~ 1 min, until the solution is homogeneous.
    • The fastest way to add the appropriate amount of ASL is to add 0.7 mL twice; that way you don't have to rotate the pipet setting in between additions.
    • A few insoluble particulates may remain. Try vortexing for another 20-30 sec interval up to four more times, and stop vortexing when the sample no longer visibly changes over that interval.
  3. Heat at 70 °C for 5 min on the heat block at the front bench.
  4. Vortex for 15 sec and centrifuge for 1 min at 20,000 rcf or 1.5 min at 16,000 rcf. Place your tubes so that weight is equally distributed in the centrifuge.
    • Unfortunately, your centrifuges cannot be set for 1.25 min exactly.
  5. Transfer 1.2 mL of supernatant into a fresh 2 mL tube.
    • Be sure to use the special 2 mL eppendorfs here and not the standard 1.5 mL eppendorf tubes.
  6. Hold the foil-covered InhibitEX tablet over the tube, and gently push until the tablet pierces through the foil and falls into the tube.
  7. Vortex until completely dissolved, which takes about 3 min for these samples.
    • The solution will be homogeneous but somewhat thick.
  8. Incubate 1 min longer on a tube stand (with no shaking), and then centrifuge for 3 min (20K g) or 4 min (16K g).
  9. Transfer the supernatant (usually about X mL) to a 1.5 mL tube and again centrifuge 3 or 4 min as needed.
  10. In a fresh 1.5 mL tube, dispense 15 μL proteinase K. Only then should you add 200 μL of the supernatant above followed by 200 μL of buffer AL, pipetting to mix each time. Finally, add 10 μL chitinase.
  11. Vortex for 15 sec (until solution is homogeneous) and incubate in the 56 °C oven for about 2 hours [1.5??].

Part 2: Writing Across the Curriculum session

During the enzymatic incubation, you will have an introductory session with our writing faculty.

Part 3: DNA extraction from bird stool, complete

  1. Quick-spin to recover sample that has condensed in the lid.
    • First time doing it, so explain quick-spinning with the usual text.
  2. Add 200 μL of ethanol, mix by briefly vortexing, and transfer to a QIAamp spin column (atop its 2 mL collection tube).
  3. Centrifuge for 1 min, and if necessary repeat the centrifugation until all the sample has gone through the column. (Unlikely in our case!)
  4. Move the spin column to a fresh 2 mL tube, add 500 μL buffer AW1, and spin 1 min.
  5. Move the spin column to a fresh 2 mL tube, add 500 μL buffer AW2, and spin 3 min.
  6. In the meantime, trim and label epp
  7. Move to yet another fresh tube and spin 1 min to rid residual buffer.
  8. Now transfer the column to your trimmed, well-labeled 1.5 mL tube and carefully pipet 150 μL buffer of AE onto the membrane.
  9. Incubate for 1 min, then spin for 1 min, cap, and store in your ice bucket. We will collect each sample and store it at -20 °C until next time.

For next time

Reagent list

write something here or not accessible to edit
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