Janet B. Matsen:Open Lab Questions

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These questions are "open" to me, not necessarily the scientific community. If you have insights or can point me toward references relevant to them, please do!

Open Questions

• What causes an overloaded colony PCR reaction to fail?
• How does plasmid copy number get affected by oxygen availability? Cellular media? I have noticed that LB often gives me orders of magnitude lower plasmid yields and that growing cultures with liquid:air volumes higher than 1:5 is not good.
• How do I decide whether to gel purify after digestions (before ligations)? The BioBrick/Ginkgo manual doesn't instruct you to. Besty always does.