How to separate fragments of similar size
Resolving fragments which have a similar size can be tricky to do on agarose gels. For example, a 30 bp difference in size between two fragments.
But, there are a few tricks you can do to help with this.
1. Use a high percentage agarose gel. Between % and % should help. Higher concentration gels have a better resolving power.
2. Create a larger agarose gel. If the gel is longer, this means the samples can be run for longer without them running off into the abyss. Longer runs mean better separation.
3. Run the electrophoresis slowly for longer. This will ensure the bands are clean and sharp. By running a gel on a high voltage can causing smearing of bands.
4. Use a polyacrylamide gel instead. Polyacrylamide gels have superior resolving capabilities (down to 10 bp!), compared to agarose gels.
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