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I'm receiving a plasmid shipped to me dried on sterile filter paper, as described in this question. This protocol and many others like it call for eluting the DNA from the paper using TE buffer.

My question is can I also use TBE to elute, as I already have a bunch on-hand? And in general, what concentration should the buffer be as I never see that mentioned in any of the protocols (including the AddGene version).

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In my experience it does not matter if you use water, TBE or TE buffer. Even with a little EDTA in it, it will not mess up enzymatic reactions as the concentration is way too low. TBE/TE buffer usually contains 1mM of EDTA which can chelate 1mM of bivalent cations. Since you not use the DNA undiluted (which also binds a lot of magnesium needed for most enzymes btw.) this really doesn't affect you in reality (been there, done that multiple times).

Additionally, I would recommend not using this DNA directly but transform it into bacteria first and then do a proper miniprep so you have enough material to work with (maybe even do a few restriction cuts and run it on a gel, to ensure the right identity) and a stock you can go back to if something goes wrong.

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This is not exactly an answer to your question, i.e., how borate ions affect storage of your plasmid DNA.

But I would recommend you to use neither TBE nor TE, as they contain EDTA that might interfere with downstream enzymatic reactions. Use water (ddH2O) instead. As long as you store your plasmid DNA at -20°C it will be perfectly stable for many years. Alternatively, use a simple Tris buffer.

Addgene has a good article on this.

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  • $\begingroup$ It really depends on the downstream applications, but the concentration of EDTA present in 1X TE (1 mM) is generally not enough to interfere with enzymatic reactions like restriction digestion, since the buffers used in those reactions supply Mg2+ at a final concentration of 10 mM or greater. EDTA chelates Mg2+ at a 1:1 stoichiometric ratio and prevents the activity of contaminating nucleases by sopping up the trace amounts of metal ions that those nucleases need as cofactors, greatly increasing the stability of DNA in aqueous solution. $\endgroup$
    – acvill
    Commented Apr 25, 2021 at 15:11
  • $\begingroup$ Yes, you're right, the final EDTA concentration in an enzymatic reactions ends up being incredibly low. Also, as @Chris points out, you would most likely want to transform the eluted plasmid in bacteria and prepare new plasmid before any downstream enzymatic reactions. $\endgroup$
    – gaspanic
    Commented Apr 25, 2021 at 15:45

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