If the electric field direction would be reversed, the migration of dendrimers would be in the opposite direction. You only have to inverse the polarity of the electrodes and maybe use an acidic buffer system. Consequently, the sample will be applied at the anodic rather than the cathodic end of the gel.

The wells serve the purpose of inserting the DNA mixture into the matrix of the gel without damaging the gel. The sample we load into the wells contains three things: water, loading dye, and DNA.

The DNA molecules have a negative charge because of the phosphate groups in their sugar-phosphate backbone, so they start moving through the matrix of the gel towards the positive pole. When the power is turned on and current is passing through the gel, the gel is said to be running.

Buffers in gel electrophoresis are used to provide ions that carry a current and to maintain the pH at a relatively constant value. These buffers have plenty of ions in them, which is necessary for the passage of electricity through them.

Glycerol is used both in sample preparation and gel formation for polyacrylamide gel electrophoresis. Glycerol (5-10%) increases the density of a sample so that the sample will layer at the bottom of a gel′s sample well.

Glycerol is known to shift the native protein ensemble to more compact states. Glycerol also inhibits protein aggregation during the refolding of many proteins. These interactions shift the native protein toward more compact conformations.

Gel wells are around 1cm deep and you generally need to substantially fill them to get enough protein onto the gel. So the stacking gel ensures that all of the proteins arrive at the running gel at the same time so proteins of the same molecular weight will migrate as tight bands.

Stacking gel has a lower pH (6.8) than the resolving gel (8.8). The purpose of stacking gel is to line up all the protein samples loaded on the gel, so that they can enter the resolving gel at the same time. The resolving gel is to separate the proteins based on their molecular weight.

SDS is an amphipathic surfactant. It denatures proteins by binding to the protein chain with its hydrocarbon tail, exposing normally buried regions and coating the protein chain with surfactant molecules.

Therefore, SDS breaks the hydrophobic interactions and hydrogen bonds, while the disulfide bridges stay intact.

SDS acts as a surfactant, masking the proteins’ intrinsic charge and conferring them very similar charge-to-mass ratios. The intrinsic charges of the proteins are negligible in comparison to the SDS loading, and the positive charges are also greatly reduced in the basic pH range of a separating gel.

Nondenaturing PAGE, also called native-PAGE, separates proteins according to their mass/charge ratio. SDS-PAGE separates proteins primarily by mass because the ionic detergent SDS denatures and binds to proteins to make them uniformly negatively charged.