southern blot probe (help......) - (Sep/05/2008 )

Hi,

In order to perform a southern blot, I have to design a probe now. is anyone knows rules for design a probe. For instance, size (I know the longer the better rule, but is there also a limitation for the size?), GC ratio, or any other rule I need to know.

Besides, I know there is different kinds of probes (DNA probe, cDNA probe and oligo probe) and many way to labeling them (Radom labeling, PCR labeling, End labeling and Nick translation). I use a virus genome to perform this experiment, and I have several target genes, the smallest is about 400bp and the biggest is about 1000bp. and i am going to label my probe with DIG. Is anyone knows which kind of probe i shall use and how should i labeling them?

Thx in advance......

Have a look at the DIG applications manual on the Roche website for details of what to do. The manual is very good and gives detailed protocols for all the different types of labelling as well as the benefits/negatives of using each.