I am trying to prepare some custom DNA binding solutions for purifying DNA with silica columns. I have prepared one with 4 M guanidine thiocyanate, 30% isopropanol, and 10 mM Phosphate buffer, pH 7.8. This worked just as well as a tris-containing commercial buffer in regards to DNA binding to the column when testing it. However, I checked the pH with a pH meter, and it is showing around pH 5.4. I am trying to study DNA modifications that are unstable at low or high pH, so I wanted to keep the pH between 7-8. The commercial buffer is around the same pH, so it seems to be consistent with this type of binding buffer. When adjusting the pH with NaOH, I didn't see much of a buffering effect also (though I am used to working with higher buffer concentrations, so maybe I added too much NaOH during that). Another commercial DNA binding buffer I checked was at pH 7.9. My questions then are, why is the pH still low in the presence of buffer, why isn't the buffer resisting pH well in this solution, and how do I get it to buffer well at the pH I want?
Thanks in advance!
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