When running an E-gel to visualize a PCR product, we can see bands on the gel because there are DNA molecules present. These DNA molecules are copies of the original PCR product, which have been amplified through the PCR process. The bands on the gel represent different sizes of DNA fragments, with larger fragments appearing closer to the top of the gel and smaller fragments appearing closer to the bottom. By comparing the band sizes to a DNA ladder or marker, we can determine the size of the PCR product.