i have been trying to resolve restriction fragments of similar length ~2kb in nondenaturing page as the difference between them is 88bp which i found very difficult in resolving in agarose gel. But the problem is that the concentrations of polyacrylamide gel which i have tried have given very confusing result.im not able to predict whether they are separating or not because i dont always see 2 bands .i run them till the bromophenol blue dye runs out of the gel and at 7V/cm.Is it possible that the restriction fragment of size 2080bp is always geting out of the gel.till now i have tried with 3.5% ,5%,6% gel and all the time i see 1 band- the 2168bp fragment?
why does the fragments get resolved sometimes and at times they dont get resolved???
how should i predict and confirm their resolution??plz help.