Final answer:
DNA does not resolve well in solution due to its large size and negative charge, clumping together. In a gel matrix like agarose during electrophoresis, DNA fragments are separated based on size as they move towards the positive electrode, with smaller fragments traveling faster. Stains are used to visualize the separated DNA.
Step-by-step explanation:
DNA does not resolve well in solution without a gel matrix because it is a large molecule with a negative charge that tends to cluster together due to its long strands and uniform charge. When subjected to gel electrophoresis, however, DNA can be separated effectively. In this technique, DNA is loaded into a porous agarose gel matrix and an electric field is applied. Due to its negative charge, DNA is pulled toward the positive electrode. The gel acts as a sieve, allowing smaller DNA fragments to move more quickly through its pores than larger ones, thus separating them based on size.
A variety of electrophoresis techniques, including pulsed-field gel electrophoresis (PFGE), can be used to separate very large DNA fragments. Moreover, the rate of migration of DNA in a gel is affected by the pore size, shape of the DNA, and molecular weight. To visualize the separated DNA, stains such as ethidium bromide or safer alternatives are used.