Preparing the gel for blotting

Following electrophoresis, the gel is usually photographed to provide a permanent record. Next, it is soaked in dilute hydrochloric acid to partially de-purinate the DNA. When the gel is later soaked in sodium hydroxide to denature the DNA, single-stranded nicks are introduced at depurinated sites in the DNA the effect of which is to fragment larger DNA segments which would otherwise blot with a much reduced efficiency. Such treatment is mandatory for the blotting of FIGE and PFGE gels.

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