Does this much salt concentration selection has a critical effect on DNA structure? Then what ideal buffer molarity should be used?
There is no ideal molarity for a buffer. It's all about the requirements. 20 mM TRIS is one of the most common buffer strengths used for solubilizing DNA. You could use any other molarity you wish. Try to think about the buffer capacity needed for the experiment you will do in future. That only could decide you buffers molarity. You could add 100-150 mM NaCl as this is also very common for DNA solutions. Salts stabilise the DNA in solution.
It is also common to include 1 mM EDTA to bind up traces of Mg2+ and other ions in order to inhibit DNase enzymes.
The commercial plasmid isolation and PCR cleanup kit include 10 mM Tris HCl pH 8.5 as elution buffer. So may be this is a good concentration and pH for DNA and wont effect the down stream processing. 1X TE (10 mM Tris HCl 1 mM EDTA pH 8.0) is used for long term preservation but EDTA might interfere with downstream processing steps.
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