A longer DNA molecule would have more phosphate groups, so it should have a greater negative charge, right? It was taught in my class that only terminal ends of DNA are charged and all the phosphates in the middle are not charged.
My teacher said that this is the reason that Electrophoresis separates the fragments. All DNA have same charge and so same force on all of them. Then difference in masses would give different acceleration and thus separation of fragments according to size. But isn’t Gel Electrophoresis more like a sieve where longer molecules move slowly and shorter pass through easily?