DNA ends after sonication - Blunt ends or not? (Feb/20/2007 )
I´m trying to perform a clonation with DNA fragments after ChIP, but I don´t know if broken DNA ends are blunt or not. If not, maybe its better to amplify by ramdom primer pcr.
Does anyone know?
As far as I know you will have a mix of 5', 3' and blunt ends after sonication.
Maybe try a restriction digest?
Something like this might also help you.
Just an example! I'm sure there are competing products from other companies as well!
If you're trying to clone, do you have an idea of a particular target gene? If so, then PCR is the best way to go. If you just want to clone everything, and decide later which clones to use, I'd try blunt-ending the DNA, rather than doing a restriction digest, and cloning the blunt-ended fragments.
Thanks you all. I want to clone all my sheared productos, and then identify them. I was thinking to treat my sheared DNA with T4 DNA polimerase or Klenow to complet posible extrems, then clone this in a vector, and finally PCR and sequencing.