Yes, it is possible to use TPE in DGGE, the concern is efficiency, which in itself depends on what you do afterwards with the recovered DNA. Because TBE is less prone to overheating, it is preferred for long runs. Borate resolves

Dear Maurice, thank you very much for your explanation

I am planing just to visualise the microbial community fingerprints and maybe cut the bands and perform the PCR for the subsequent sequencing.

Will the phosphate interfere with this task without DNA purification?

Dear Mikhail

You can also go with the following preparations, whichever is convenient with your design

1) SB Buffer – 10 mM sodium boric acid (1X working solution is either 5 mM disodium borate decahydrate or 10 mM NaOH adjusted to pH 8.5 with boric acid; up to 50X concentrates can be made. 20X concentrate should have a pH of 8.0 → for more details see the manuscript below)

(2) LA Buffer – 5 mM lithium acetate

(3) LB Buffer – 1 mM lithium boric acid (lithium hydroxide pH buffered to pH ~8.5 with boric acid)

The advantages of these buffers are multiple; (a) they generate much less heat than TAE or TBE buffers, (b) they can be run at much high voltages (>300V in some cases) without fear of gels melting, (c) they can be much cheaper than TAE or TBE, (d) they do not interfere with standard applications such as band excision, and (e) they last longer before needing to be replaced.