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I need to remove any traces of linear DNA (both single and double stranded) from a ligation reaction while keeping circular DNA intact. Up to now, I have used Epicentre's Plasmid Safe to do the job. I would like to try another solution (mostly because of the unreliability of our supplier: it takes weeks to get a batch!).

Has anyone replaced Plasmid Safe with other nucleases? Which one? I have been looking at the NEB nucleases and I was thinking to use ExoV and T together to get rid of any linear DNA (both ssDNA and dsDNA). Does anyone have any other solution to propose?

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    $\begingroup$ "any other solution" How about separating them on a gel? $\endgroup$ – canadianer Jul 17 '17 at 14:40
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    $\begingroup$ I would like to avoid gel-purification, the input DNA is already low, plus, some linear DNA is running at the same height of the circular one. I really need to digest specifically the linear ss and ds DNA. $\endgroup$ – alec_djinn Jul 17 '17 at 15:14
  • $\begingroup$ alec_djinn, did combining ExoV and T work for you? I am also looking for methods alternative to Plasmid Safe. Thank you! $\endgroup$ – Rina_lee Jan 17 '18 at 23:25
  • $\begingroup$ Yes, it worked. All the linear DNA is digested. But be careful to do not let the reaction go too long. In my case, 15 min was enough to digest 500 ng with 5 units of both enzymes. Try it out. $\endgroup$ – alec_djinn Jan 18 '18 at 6:37

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