gDNA restriction digest - (Oct/08/2010 )
I'm a bit confused. I'm attempting to perform a partial restriction digest of gDNA. but What should this look like on a gel? i want bands between 1kb-12kb. Should it just be a a smear in my size range? And Should there be undigested gDNA visible? Also what would a complete digestion of the gDNA look like?I am restricting with EcoRI
Many thanks for your time!
It depends on DNA (i.e. species) and the enzymes you use. EcoRI is normally a frequent cutter (i.e., the recognition site has six base pairs frequently occurring in the genome) and will produce a lot of smaller fragments, resulting in a smear on the gel. If you use enzymes whose recognition sequences are less frequent in your DNA, then you'll get larger fragments, and also less (some enzymes might even not cut at all).
Normally you have to try out which enzyme(s) produce the range of fragment sizes you need. Or you find a publication with some information about this.