When we eat food I heard that our digestive enzymes disassemble the DNA of the eaten cells so that the DNA cannot affect us. Then, is there any mechanism (that prevents the eaten cell's DNA from affecting us genetically) in cell-scale level? Or is it only in organ-system level(e.g. digestive system)? It seems that germs and viruses don't have the mechanism, as we manipulate them as genetic transferor. But I want to know if nucleate cells have the mechanism.
Cells have cell membranes and sometimes cell walls that keep random molecules from entering the cell. Only small, uncharged molecules can pass freely through the membrane. Complex structures of proteins embedded in the cell membrane regulate the passage of charged or large molecules. Pathogens like viruses or bacteria have had developed equally complex structures of proteins that can fool the proteins in the cell membrane to gain access to the interior of the cell. In other words, the cell membrane is almost always going to keep naked DNA from entering the cell, but viruses can get around this, by packaging their DNA in protein capsules that can compromise the cell membrane.
To create GMO, viruses are often used to transport the foreign DNA into the cell. Alternatively, the cell membrane can be attacked with chemicals, high voltages, or even mechanically punched holes, that allow DNA to pass through the membrane.
Bacterial cells will sometimes allow the passage of naked DNA, but this is very rare in plant and animal cells.