What were the findings of the studies that investigated nucleic acids in agarose gel?
A large number of studies have been conducted to investigate the specific movement of nucleic acids through agarose and polyacrylamide gels when exposed to a constant electrical field. Ogston concluded that nucleic acids perform a “particular mode of transport” when being separated electrophoretically through a gel matrix, which has since been dubbed Ogston sieving. It is the “radius of gyration” that governs the movement of the nucleic acid through the gel, and the more similarity in size there is between this and the pore size, the more likely it is the molecule will pass through. For this reason, it is extremely hard to separate the smallest fragments as they act as if there is no gel present. In comparison, fragments of an intermediate size experience numerous collisions with the gel matrix resulting in their separation from smaller molecules which will be able to migrate farther because they experience less frequent collisions.
Another format of nucleic acid migration is reptation. De Gennes coined the term ‘reptation’ which describes how, initially, nucleic acids can “deform and enter the gel ‘end-on’”. De Gennes illustrates how molecules move through the gel in a way similar to that of reptiles; indeed, a snake-like migration. Although the cross-sectional area of the molecules is irrelevant if they are positioned end-on, the ability to separate nucleic acids by size is important because fragments need to meander through the pores in the gel. Thus, a smaller fragment will move much more quickly and farther than a fragment of a larger size.