I have 600bp long DNA, digested with Restriction enzyme to create 2 fragments one is 500bp long and another is 100bp long I want to see both the bands, so what percentage of agarose gel should I use?
2-3% use 3% for clear identification of smaller band. Note: Use the higher concentration of DNA for digestion.
Addionately to higher percentage gel you can also use special agarose which seperate low bp/small DNa fragments. Good luck!
2% agarose would be better for your gel run. you can easy visualize the difference of 400bp DNA fragment in 2% agarose gel.
2% agarose gel will be perfect to separate both the bands on one gel in single run.
In our lab we use to do 2.5% agarose gel to separate smaller fragments.
Agarose gel of 2.5 - 3 % can be used to separate smaller fragments.
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