Hello
I am trying to cut a segment from a plasmid that is around 80 and I wonder if I could see it on the gel taking in consideration that the smallest size on the ladder is 100 bp. however, I just want to know If i could see a band under 100 bp as that would help me to choose which colony is going to sequencing. maybe if I use 3% agarose gel? I use ethidium bromide and TAE as a buffer.
Yes, you should be able to see this band. Use at least 3% agarose (preferably 4%).
Yes, besides the 4% agarose suggested by Martin Lenicek , you will need a 25 bp resolution ladder.
Yes it will be visible but as well as 3-4% agarose it would be best to cool the gel and buffer and run the gel at half your usual current to avoid warming the gel and minimising thermal diffusion of the small band. If no cold room is available then just halve the voltage that you normally use. At least the separation of plasmid andinsert will be very great
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