Correcting for AFM tip induced topography convolutions in protein–DNA samples

Atomic force microscopy (AFM) imaging offers information on many unique parameters of protein–DNA complexes. However, exact lateral dimensions of molecules or protein assemblies are convoluted with the finite size of the mechanical imaging probe, the AFM tip. An approximate knowledge of the tip dimensions allows correction for these convolutions. In the past, a variety of standards for tip size evaluation have been described, such as metal beads or nanotubes. In the context of protein–DNA samples, being able to exploit the DNA directly for such lateral image (length) corrections without the need to apply additional calibration particles is highly desirable, avoiding crowding and confusion in the images. Here, we systematically evaluate and compare simple geometrical model approaches for DNA as a lateral calibration standard in AFM imaging.