Matt:LabNotes/2014-6-19: Difference between revisions

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==Check Agi26k0gap Oligos for DpnII Restriction Sites==
==Check Agi26k0gap Oligos for DpnII Restriction Sites==
*Lambda exonuclease digestion has been having low efficiency [[Matt:LabNotes/2014-5-22#Probe_Expansion_PCR | Try 1]] and [[Matt:LabNotes/2014-6-11#Lambda_Exonuclease_Digestion | Try 2]]
**Dr. Zhang suggested skipping lambda if very few oligos would be digested
*Used [[File:ProbesWithDpnIISites.txt | ProbesWithDpnIISites.pl]] to identify oligos with extra DpnII site
*Used [[File:ProbesWithDpnIISites.txt | ProbesWithDpnIISites.pl]] to identify oligos with extra DpnII site
*Oligos identified by line # in the [[File:ProbesWithDpnII.txt | text output]]
*Oligos identified by line # in the [[File:ProbesWithDpnII.txt | text output]]
*Of 12,964 oligos, 8,744 (67%) have DpnII restriction sites besides the intended cleavage site
*Of 12,964 oligos, 8,744 (67%) have DpnII restriction sites besides the intended cleavage site
**'''Conclusion:''' cannot skip lambda digestion step

Latest revision as of 01:40, 20 June 2014

Check Agi26k0gap Oligos for DpnII Restriction Sites[edit]

  • Lambda exonuclease digestion has been having low efficiency Try 1 and Try 2
    • Dr. Zhang suggested skipping lambda if very few oligos would be digested
  • Of 12,964 oligos, 8,744 (67%) have DpnII restriction sites besides the intended cleavage site
    • Conclusion: cannot skip lambda digestion step