AlanFung:LabNotes/CTCF/2011-5-10

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Bisulfite Conversion DNA Damage Estimation

  • Perform PCR with CHR8, CHR21 and CHR22
  • These will be our standards

File:ZhangLab 2 2011-05-10 10hr 40min.jpg

  • Need to purify CHR8, CHR21, and CHR22.
    • Qubit Results(ng/ul)
    • Assume amplicon length ~200bp
  • CHR8-3.25ng/ul 26.72nM
  • CHR21-4.39ng/ul 36.09nM
  • CHR22-4.77ng/ul 39.21nM


  • Run an experiment where we do PCR on both Bisulfite-converted DNA and the three controls
    • Want to make sure number of starting molecules is the same.
  • With normal DNA, 5 pg ~= 2 molecules
  • With PCR product, X pg ~= 2 molecules; X << 5
  • Need to run a PCR reaction using 500 pg of bisulfite converted DNA and X pg of PCR product as templates, with X such that the number of molecules in each tube is the same.
    • Can run QPCR to check for DNA damage; only hot-start for 30 seconds instead of 3 minutes.