The agarose obstacle course

The DNA race occurring in an electrophoresis gel is fair but it is an obstacle course. This is because the DNA molecules are forced to travel through the matrix of buffer filled spaces or pores that is created when the agarose gel is formed. The agarose gel provides a three dimensional lane. A random mix of small and large spaces will be found in any given part of the lane. If a DNA molecule cannot fit through a pore it moves up, or down to find a pore big enough to squeeze through. The molecule does not take a straight path to the positive end of the gel but instead wiggles through (Fig. 15). Shorter DNA segments find more pores that they can wiggle through, longer DNA segments need to do more squeezing and up or down moving. For this reason, shorter DNA segments move through their lane at a faster rate than longer DNA segments. That is why the gel electrophoresis method separates DNA molecules based on their size.

Fig. 15. DNA fragments move through the gel by weaving in and out of the gel pours. (Image by D. Lee)