I am trying to bind my plasmid DNA to silica columns. 4.5 M Guanidine Thiocyanate, 1 M K acetate PH adjusted to 4.2 does not work for me but ph 3.45 works, however 260/230 ratio is bad-0.5 to 0.7 is that the PH or Guanidine or alcohol that interferes?
pH 3.6 could be damaging if you incubate for longer periods. I don't quite understand though why DNA won't bind at higher pH . As far as I can tell all Qiagen DNA purification kits are based on this.
What is the size of your plasmid? Are you trying to bind a pure plasmid or you performing lysis from tranofmed cells? From your OD readings it looks that have quite a bit of protein and salts carry over. DNA is quite resiliant to damage, but what you are working with is quite low for binding conditions, unless the presence of proteins is aiding such binding.
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