Hi,

effective range of separation (ie 6-100 bp for 20% gel) means, that it can be used for fragments of the total size within this range (not differing by 6-100 bp). In your case, you should use less concentrated gel - something about 5% should work. Longer gel might be needed, as the difference between both fragments is quite small. If you will not succeed with mini or midi PAGE, think about running fragment analysis on a sequencing machine.

Martin

Hi Martin,

thanks for the answer. if the range of separation is the total size of fragment, then what is the resolution of a typical page on say a mini gel( the least size difference that can be detected )?

regards

I would guess, 5% difference should be easily visible. If you let proceed it for a long time (allowing your bands to travel through the whole gel) resolution should be better than that. I would start with 7% gel (29:1 acrylamide:bis) - if not sufficient, you can alter acrylamide:bisacrylamide ratio (add more bis eg 25:5). Alternatively, there are some PAGE additives, that greatly improve resolution, however, you should be able to resolve your fragments without it.

is there an enzyme which cuts one fragment and not the other so you will be separating large from small. Or possibly cuts both but the separation is , for example, 150 from 169...and a constant band (or more). this would be a much easier separation?