User:Kathryn Muratore/Notebook/AU CHEM-570 lab prep/2011/06/24: Difference between revisions

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# Gel purification did not work
# Gel purification did not work
#* Also, note that there is a lot of ethanol in these solutions.
#* Also, note that there is a lot of ethanol in these solutions.
## ''Solution'' - check [DNA] by UV (1:10 dilution should give A<sub>260</sub>=0.05-0.1 according to gel estimates.
## ''Solution'' - check [DNA] by UV (1:10 dilution should give A<sub>260</sub>=0.05-0.1 according to gel estimates based on mass, but will not be visible based on moles.
##* Do this today!
##* Do this today!
#* Recall that I did not incubate the melted agarose sample in the column before applying a vacuum.  
#* Recall that I did not incubate the melted agarose sample in the column before applying a vacuum.  

Revision as of 12:35, 24 June 2011

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Bench work

  1. Check [DNA] of gel-purified samples from 3 days ago
    1. 95μL H2O + 5μL each DNA sample (ddI, ddV(His), and ddV)
      • → measure A260 and A280
  2. Plate remaining 800μL of each transformation from 2 days ago
    • → rt over the weekend
    • I should have plated this yesterday and grown O/N, but I forgot.

Conclusions and future plans

Possible problems:

  1. Ligation worked, but transformation did not.
    • Solution - transform the ligation product into User:Matt Hartings commercial competent cells
  2. Ligation did not work, but gel purification did work
    1. Solution - try to re-ligate again with the correct [DNA] and using the longer incubation at 16°C
  3. Gel purification did not work
    • Also, note that there is a lot of ethanol in these solutions.
    1. Solution - check [DNA] by UV (1:10 dilution should give A260=0.05-0.1 according to gel estimates based on mass, but will not be visible based on moles.
      • Do this today!
    • Recall that I did not incubate the melted agarose sample in the column before applying a vacuum.
    1. Solution - repeat all steps starting with NheI digestion!
      • This is the last resort and only if UV data is inconclusive or shows no DNA.
      • I should be able to use less restriction enzyme in each step. I don't think this caused any problems, but I only have 10μL of SapI left and have been over-digesting with 10U for <1μg of DNA, so I could definitely cut back and still get complete digestion without ordering more at this time.
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