I know that the two columns are silica-membrane based, but perhaps they bind different sizes of DNA? I am extracting DNA from intestinal content samples for microbial community analyses, and the yield is always quite low anyway, so i'm wondering if the QIAquick columns can be used instead of/in addition to the QIAamp spin columns? Thank you
A lot of columns for a lot of kits from manufacturers like Qiagen are fairly interchangeable. Contact the company and explain your situation and see what they say. Even if the columns can not be swapped directly, they may have a suggestion for an altered protocol that will allow you to use the QIAquick columns for what you are seeking to do.
Go through the following link, hopefully it will help you
http://huazhongwei.wordpress.com/2011/07/29/the-purified-genomic/
I wouldn't hesitate to exchange it.
The binding capacity is limited through the resin volume, if it is the same volume = height, you can assume same capacity. The length cutoff for the binding DNA is driven by the buffer composition (chaotropic salt vs. alcohol), assuming both columns use silica membranes (which they undoubtedly do).
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