"judas" <jiriki at primus.com.au> wrote:
>Would someone mind helping me out with a question, specifically why when the
>linear lambda genome is run on a gel with ethidium bromide, the 4.36Kb
>fragment from the right end should appear faint compared to the rest of the
>fragments. I think it has something to do with the cos sites?
I suppose you mean HindIII digested Lambda DNA.
Normally, the EtBr-stained DNA loses intensity with its length,
i.e., small frag. weak intensity and large frags strong intensity.
The 4.3 fragment sticks to the largest fragment which itself
already shows the most intensive staining, so the additional
4.3 fragment does not influence the intensity significantly.
The retarded migration of the big frag. with an attached 4.3
can hardly be seen in a gel because big frags separate
not as efficiently as small ones (logarith. correaltion:
DNA-size vs migration)
Hope that helps,