I'm trying to purify a DNA fragment of 12,8Kb from low melting agarose gel. Although I know that yield is importantly altered by DNA fragment size. I have had a lot of issues purifying this fragment and I would like to know if staining with those methods can have an effect on purification yield since the most of the protocols that I have checked recommend staining with Ethidium bromide.
All of these dyes are intercalators and so should not interfere with purification. How are you doing the purification? There are several methods available, I use to do dialysis for fragments above 15 kb and use a PCR and Gel spin column for anything smaller, both methods worked very well and gave good yield with both ethidium bromide and SYBR Safe.
In my experience no. The only caveat I can think of is that visualisation by uv light causes nicking and/or breaks bit this is just really ethidium bromide doesn't happen without uv light and in any case doesn't effect recovery in my experience of visible versus uv dyes
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