Some Practical Considerations
1. It's essential to prepare the electrophoresis buffer and gel fresh for each run. Make sure the cutting table is clean, and the blade is properly sterilized. This helps prevent any foreign DNA contamination in the cut gel piece.
2. When excising the gel, make sure to recover all of the gel containing the target DNA fragment. To minimize the amount of gel used, you can use a thinner gel layer, as long as it’s thick enough to be handled easily. A thin and wide comb can also be used to help spread the gel evenly during running.
3. For protection, wearing regular plexiglass shields is usually sufficient. However, it's recommended to wear a protective mask and eye protection, such as resin glasses, especially when working with UV light or chemicals like ethidium bromide (EB).
If you're particularly concerned about UV exposure or need an EB-free alternative, you can use a marker and a ruler to take a photo under UV light. This helps you accurately locate the target band on the gel before cutting.
Follow the standard procedure: first, mark the gel using a marker, then stain it with EB, and finally take a photo with a ruler placed next to the gel under UV light. Since the relative position between the target band and the marker is known, you can measure the exact location of the band on the unstained gel.
If it's hard to determine the position visually, you can lightly mark the gel directly on the marker, which makes it much easier to identify the correct area for excision. This small step can save time and reduce errors in the recovery process.
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