PEGylated surfaces for the study of DNA-protein interactions by atomic force microscopy

Abstract

DNA-protein interactions are vital to cellular function, with key roles in the regulation of gene expression and genome maintenance. Atomic force microscopy (AFM) offers the ability to visualize DNA-protein interactions at nanometre resolution in near-physiological buffers, but it requires that the DNA be adhered to the surface of a solid substrate. This presents a problem when working at biologically relevant protein concentrations, where protein may be present at large excess in solution; much of the biophysically relevant information can therefore be occluded by non-specific protein binding to the underlying substrate. Here we explore the use of PLLx-b-PEGy block copolymers to achieve selective adsorption of DNA on a mica surface. Through varying both the number of lysine and ethylene glycol residues in the block copolymers, we show selective adsorption of DNA on mica that is functionalized with a PLL10-b-PEG113 / PLL1000-2000 mixture as viewed by AFM imaging in a solution containing high concentrations of streptavidin. We show that this selective adsorption extends to DNA-protein complexes, through the use of biotinylated DNA and streptavidin, and demonstrate that DNA-bound streptavidin can be unambiguously distinguished by in-liquid AFM in spite of an excess of unbound streptavidin in solution.