Self-assembled DNA nanostructures for distance-dependent multivalent ligand–protein binding

An important goal of nanotechnology is to assemble multiple molecules while controlling the spacing between them. Of particular interest is the phenomenon of multivalency, which is characterized by simultaneous binding of multiple ligands on one biological entity to multiple receptors on another1. Various approaches have been developed to engineer multivalency by linking multiple ligands together2,3,4. However, the effects of well-controlled inter-ligand distances on multivalency are less well understood. Recent progress in self-assembling DNA nanostructures with spatial and sequence addressability5,6,7,8,9,10,11,12 has made deterministic positioning of different molecular species possible8,11,12,13. Here we show that distance-dependent multivalent binding effects can be systematically investigated by incorporating multiple-affinity ligands into DNA nanostructures with precise nanometre spatial control. Using atomic force microscopy, we demonstrate direct visualization of high-affinity bivalent ligands being used as pincers to capture and display protein molecules on a nanoarray. These results illustrate the potential of using designer DNA nanoscaffolds to engineer more complex and interactive biomolecular networks. DNA tiles can be used as a platform to display two different aptamers — short sequences of nucleotides that bind to proteins — with high spatial control, to systematically study the distance dependence of multivalent interactions.