Please don't ever try to use absulute ethanol which is less than 96% to 100%. In an 95% ethanol or worse still the denatured ethanol, it contains at least 5% of impurities such as methanol, butane and isopropanol which might not evaporate efficienctly on dry spin column.
This is critical as ethanol is needed to wash away the salt used in the purification process, and imagine what will happen if the spin column does not dried completely prior to the elution steps..... Lot's of salt and other chemical that are present in the reagent (s) used in previous step of extraction and purification. After all, what is the point of performing a washing step prior to elution if most of the salt (s) or regent (s) can't be effectively been washed away???
And perhaps you might wish to list out what is the potential salt (s) or reagent (s) that could be carried over, which will detrimentally affecting your downstream assay?
A quick check, perhaps you can have a look at the A260/ A230 ratio of the purified nucleic acids that you have.
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