Separation of DNA (4731bp and 4690bp) - (Feb/26/2006 )

I wonder if I can separate 4731bp and 4690bp by any kind of gel electrophoresis.

These are the restriction products of the expression vector by BamH1 and HindIII. I wonder if the vector is digested by the two enzymes and I need to isolate the double digested one which is 4690bp.

I tried %0,5 - %1 - %2 and %3 agarose gel electroporesis about 3 hours, 80V in TAE but only one band was seen below the 5000bp marker band in %0,5 and %1 agarose gel. I did not see the 40bp (the other restricted product of the vector located between the two restriction sites) in all tried gel concentrations. I controlled at every 45min. for 40bp not to pass through the gel.

Thank you.

once i tried to seperate 2961bp (pBluescriptII KS+) and 2789 bp (my insert) from 0.5% gel by 50 volt for a long time. upto 2000bp was pass though the gel but i failed to seperate my target fragment as only one band was seen in the gel.

I am facing the similar problem. I use the third enzyme to digest vector into smaller fragments.