I want to use a library prep kit that will allow relatively unbiased sequencing of dsDNA and ssDNA viruses. Unfortunately the kit doesn't come with a way of shearing the viral DNA to the correct length and I don't have access to an ultrasonicator. There is a NEB kit for enzymatic shearing but this will only do dsDNA. Does anyone have any suggestions?
Tyler Chafin
You can try passing the DNA through a fine hypodermic needle. You will need to experiment with the gauge and number of passes to get to your desired level of fragmentation, but its a cheap solution.
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Anirudha Sahu
Try using Micro-coccal nuclease (mostly prefers single-stranded nucleic acids but also acts on ds DNA) @ 370 C for 20 minutes.
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