Agarose is a sugar that is derived from seaweed. It is often used for the electrophoresis of nucleic acids, like
DNA and
RNA. Typically, the agar is dissolved in water, then heated up and poured into the casting for the electrophoresis matrix. The sugar chains cross link to form a type of web that the
DNA must move through. The higher concentration of agarose that is used, the smaller the holes will be, so the more difficult it becomes for larger pieces of
DNA to move through the matrix. Varying the concentration of agarose varies the resolving power of the gel. At higher concentrations, the gel can resolve smaller pieces of
DNA, so if you have a collection of fairly short segments of
DNA, a high concentration agarose gel will give you clearer bands and better separation. Similarly, low concentrations of agarose are said to have low resolving power. This is best if you have
DNA with a variety of sizes, but if you have just small
DNA, it will most likely just form a messy, thick band towards the bottom of the gel.