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As pointed out by aandreev, the greater the size of the insert relative to the flanks lower will be the recombination rate. This is because the donor DNA essentially becomes non-homologous. See the figures below:                 Figure1: Effect of insert size on recombination ...


In my view there is direct link between probability of recombination and size of the insert. Smaller inserts with larger flanks get incorporated easier. That I understand from reviewing studies based on Cas9/CRISPRs system. Same should stand for HR-mutagenesis in yeast. So, short answer will be: shorter inserts are more efficient. However, I couldn't find ...


You will definitely get satellite colonies. Ampicillin breaks down after about a day, especially exposed to light. Kan, keeps pretty well at room temp, but that does you no good :)

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