RE (MspI) Digestion of PCR Products

[Clinton Edwards]

Ive also had problems in cutting DNA fragments in the past. I dont think 
its a good idea to cut fragments without purifying first. i.e: Magnesium 
ions may inhibit the enzyme, and even if you add the reaction buffer, the 
PCR reaction buffer is still present and will add/alter reaction buffer 
components. Also, in my experience, cleaning the DNA with organic 
solvents can often inhibit the R.E if you are not carefull. If you can 
get hold of one, try using Qiagen's PCR purification columns, to remove 
un-used primers, Taq,  etc, and elute with water (The procedure takes only 
about 3 minutes). This way, you know other components like TE buffer, 
Phenol/chloroform etc wont interfer. BamH1 has given me problems like 
yours, until I tried using these columns.

Good Luck!

Clinton