Probing biomolecular recognition using atomic force microscopy

Atomic force microscopy (AFM) can be used to investigate the mechanics of molecular recognition between biological molecules, when one or both of the binding partners were immobilized to a solid support. The topography of the surfaces, as well as the adhesive strength and specificity of the biomolecular interactions were examined. Discrimination between chemically distinct surface-bound biomolecules was simplified by the use of a patterned support, or array, through the spatial control of ligand presentation.; In the AFM application known as “chemical force” microscopy (CFM), a chemically modified AFM tip is used to probe a substrate array through chemical recognition. When modified with a biological ligand or receptor, the AFM tip can differentiate its biological binding partner from the other molecules on a heterogeneous substrate. The strength of the interaction between the modified tip and the substrate is governed by the molecular affinity. CFM was used to probe the interactions between short segments of single-stranded DNA (oligonucleotides). The substrates consisted of micron-scale, patterned arrays of one or more distinct oligonucleotides. When a DNA-modified tip was scanned across the array, a strong friction interaction was measured between the tip and the surface. Complementary oligonucleotides exhibited a stronger friction force than the non-complementary sequences within the substrate array. The friction force correlates with the measured adhesion (rupture) force for the oligonucleotide pairs. The surface energy of this interaction is consistent with the formation of hydrogen bonds, suggesting that the friction and adhesion arise from a sequence-specific interaction (hybridization) of the tip- and surface-bound DNA.