[lily_m]

Hello all, i was wondering if someone could help me with this one? What is the basis for the binding of DNA to the matrix used in the purification procedure? (procedure is re-electrophoresis of DNA sample)

[renge ishyo]

For electrophoresis in general, the matrix forms little holes or pores for the molecules to get stuck in as they travel across the gel. Depending on the size of the holes, they can slow down molecules at different rates (which in turn depends on the size of the molecule). It is sort of like how a typical speedbump in a supermarket parking lot will slow down a lowrider more than a Geo Metro which will in turn be slowed down more than a monster truck as each passes the *Ignore me, I am impatient*. If you remove the speedbump all three could travel at the same rate, but the speedbump changes that (the analogy isn't perfect because the smaller DNA fragments should travel across the gel faster than heavier ones, but the idea is similar). You can alter the size of the holes on the matrix to get different weights of molecules to separate from one another in any "weight range" you like (usually by changing the amount of gel crosslinking that takes place when forming the matrix).

As far as I can tell this effect does not require an actual bond from DNA to matrix per say, it's more like having a rough frictional surface to travel over with "potholes" of a certain size that affect some molecules more so than others.

[lily_m]

Thank you so much