Haynes Lab:Notebook/Engineering PC-TFs/2013/09/26

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(September 26, 2013)
(September 26, 2013)
Line 29: Line 29:
''PEG/MgCl<sub>2</sub> Precipitation''
''PEG/MgCl<sub>2</sub> Precipitation''
 +
* This procedure was adapated from [http://openwetware.org/wiki/Protocol_Size_selective_DNA_precipitation_by_PEG/MgCl2 Size selective DNA precipitation]
*Measure the following into 1.5 mL tubes.
*Measure the following into 1.5 mL tubes.
Line 72: Line 73:
[[Image:hiddendragonsofthetemple.jpg|250px|CMV PEG/MgCl<sub>2</sub> Precipitation 9/26/2013]]
[[Image:hiddendragonsofthetemple.jpg|250px|CMV PEG/MgCl<sub>2</sub> Precipitation 9/26/2013]]
 +
 +
The higher the final PEG concentration, the smaller the fragments that will stay in the supernatant. According to the protocol at  [http://openwetware.org/wiki/Protocol_Size_selective_DNA_precipitation_by_PEG/MgCl2 Size selective DNA precipitation] the sizes of the DNA that should remain in the supernatant are:
 +
* 10% PEG, > 300bp in supernatant
 +
* 6% PEG, > 500bp
 +
* 5% PEG, > 700bp
 +
* 4% PEG, > 1kb

Revision as of 13:18, 27 September 2013



Main project page
Previous entry      Next entry

September 26, 2013

Restriction Digest

  • Perform restriction digest for CMV promoter
Reagent Volume
DNA (plasmid) 10 μL
XbaI 1.0 μL
PstI 1.0 μL
Green 10x FastDigest buffer 3.0 μL
dH2O 15 μL
  30 μL --> 37°C/ ~10 min.

PEG/MgCl2 Precipitation

  • Measure the following into 1.5 mL tubes.
Reagent 15% 10% 7% 5% 2%
30% PEG 50 μL 33 μL 23 μL 17 μL 7 μL
DNA 15μL15 μL15 μL15 μL15 μL
dH2O 35 μL52 μL62 μL68 μL78 μL
Total 100 μL 100 μL 100 μL 100 μL 100 μL
  • Centrifuge for 15 minutes at 10,000g.

DNA Clean & Concentrator

  • Although there was no pellet, ran a DNA Clean & Concentrator on samples.
    • Add 2 volumes of DNA Binder Buffer to each DNA sample (200 μL).
    • Place mixture in spin column into 2 ml collection tube.
    • Centrifuge at full speed for 30 seconds.
    • Add 20 μL of DNA Wash Buffer and centrifuge for 30 seconds. Repeat this step.
    • Place Zymo-Spin Column into a new 1.5 ml tube. Add 20 μL of water directly to column matrix and spin to elute DNA.

Gel Electrophoresis

  • Follow steps for gel electrophoresis.
  • Orient top notch of gel electrophoresis apparatus. Place gel tray into larger tray.
  • Fill gel flask with up to 60 ml of TA buffer.
  • Create 1% gel by putting .6 grams of agarose into flask.
  • Microwave agarose solution for 40 seconds
  • Using hot gloves, grab flask out of microwave and swirl flask vigorously. Place back in microwave for 40 more seconds.
  • When flask is taken out of microwave, make sure that the agarose is completed dissolved.
  • Set up wells on gel electrophoresis apparatus. The mold for the first digest is B-10. Use the thick "teeth" and slip in the notches.
  • Add EtBr (ethidium bromide) to the agarose gel. There should be 1 microliter of EtBr per 10ml of agarose gel. Therefore, 6 µL.
  • Pour gel into tray.
  • Wash the agarose gel flask.
  • Run gel for 45 min at 100 V. Check gel under UV light.

CMV PEG/MgCl2 Precipitation 9/26/2013

The higher the final PEG concentration, the smaller the fragments that will stay in the supernatant. According to the protocol at Size selective DNA precipitation the sizes of the DNA that should remain in the supernatant are:

  • 10% PEG, > 300bp in supernatant
  • 6% PEG, > 500bp
  • 5% PEG, > 700bp
  • 4% PEG, > 1kb



Personal tools