Southern blot problem - probe-target short compatibility region (Feb/13/2005 )

Hi everyone!

I am trying to detect some positive ligation products using PCR amplification and Southern dot blot, and it turned out that there are only 250 identical bp expected between the probe and the target. So my question is: will it work or will not?

Thanks in advance

Youlia

hi youlia
i belive it will - basicly you can get signal even with oligos about 20bp long. if your non-homologus sequnce is very long it may interfere though. if you have some of your probe DNA non-labelled use that for positive control and then you'll know for sure!