co - migration of PCR products

[vondrakl]

Hi,
i have a question.
I have two PCR amplicons of nearly identical size (173 and 186 bp) received by multiplex PCR and i'm interested if it is possible that they co - migrate in agarose gel electrophoresis. When there is only 186 bp product in the gel its position is a little bit higher than when there are this two PCR amplicons (173 and 186 bp) together.

Do you know something about this phenomena? thank you for yours replies

[luisillo]

If you want your fragments to separate enough to be visualizable you will have to increased the agarose concentration of you gel, that way the bands will appear less diffuse (or more compact, whatever) being easier to identify both of them. Also, run the electrophoresis for more time so that the fragments be able to separate form each other (both conditions, gel conc and time, have to be standarized).

By the way, polyacrilamide gels gives you better resolution for fragment separation.