the sample using gel electrophoresis. After that, I sonicate the sample but when I want to cut gel
Some more info is needed here. How much and what size distribution of DNA did you recover? Did you remove possible sources of endonuclease activity and store your DNA in TE buffer? How are you choosing sonication parameters?
Without this info, it is impossible to assess whether your DNA degraded prior to or during sonication, or whether you over-sonicated your DNA, or whether you simply have too little DNA to detect on a gel following sonication.
I am trying to recover DNA with a size of about 20kb. I didn't store in TE buffer but I store in sterile ultrapure water. For the sonication part, I already did some preliminary test before. I used 80% power with 30% duty and sonicated for 20s. I already loaded in 18uL of the samples but still cannot see the band.
How much DNA did you have prior to sonication? How well could you see it on a gel?
I used about 30uL of DNA sample for sonication. Before sonication, I can see the band with about 20uL of the sample.
What size was the band prior to sonication? You mention that you expect the DNA to be 20kb. It this what you observe on the gel?
Maybe you could enclose the gel image, so that us can be more clear about your problem
Yen- since you are starting out with a complex mixture of DNA (note how smeared your original sample is), I would not expect to see enrichment for a particular sized band upon sonication. Sonication will shear your DNA into much smaller fragments, but these will be heterogeneous in size also. Is your goal to sequence this material?
Yen- please take a look at this pre-existing thread:
https://www.researchgate.net/post/Metagenomics_Problem
I think it may contain some technical pointers that will help you achieve better results!
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