Interactions of nuclear acids with cell membranes are at the heart of numerous biomedical and nanotechnological applications of DNA and DNA-based nanodevices. Despite enormous recent development in DNA nanotechnology, very little is known about DNA–membrane interactions at a molecular level. Here we employ biased atomic-scale computer simulations to calculate for the first time the free energy profile for partitioning a DNA molecule into a phospholipid bilayer, a system that is routinely used to mimic the properties of cell membranes. Our findings clearly show that a zwitterionic lipid bilayer represents a repulsive barrier for DNA: the potential of the mean force profile does not develop any local minima upon moving DNA from water into the lipid/water interface. This energetic barrier can be overcome e.g. via adsorption of divalent calcium ions on the surface of a lipid bilayer, which makes the lipid bilayer effectively cationic. Indeed, our biased molecular dynamics simulations confirm that the correspondin