I'm using cDNA AFLP teq.. I extracted 670 bp band from polyacrylamide (urea) gel and I have amplified with PCR but on agarose gel it stops at nearly 350 bp.it happened for most of other bands before. I always extracted the precise bands. I repeated with both pre and selective primers with the same PCR program before done for amplification of digested cDNA and same size bands observed in agarose gel.I wonder maybe secondary structure causes losses in band size (before running in polyacrylamide samples treated in 94 degree for 5 min), but how I can recognize? i should notice 350 bp band i mentioned above is very sharp. what other thing I'm wondering is can dye uses in agarose gel alternate the DNA charge and reduces the speed of movement . The big matter is the rate of losses in band size almost is same for almost all of the bands for one primer. Is it happened for anyone before? can i trust on my extracted bands for doing cloning?