The predictable geometries and intermolecular interactions of DNA have led to the development of many arbitrary nanoscale objects, including a class termed DNA origami. DNA origami nanostructure fabrication occurs through the folding of long, single-stranded DNA using short, single stranded oligonucleotides. Detailed herein is the development and characterization of DNA origami nanostructures with site-specific modifications for aptamer-mediated binding of target molecules. Molecular self-assembly is performed by thermal annealing and fabricated objects are purified by centrifugal filtration through molecular weight cut-off membranes. Nanostructures are characterized by agarose gel electrophoresis, UV-Vis quantification, and visualization by atomic force microscopy. Thrombin-binding aptamers, TBA15 and TBA29, were captured to the surface of rectangular DNA origami nanostructures and were incubated with the target, thrombin, to demonstrate the site-specific binding of target molecules. DNA origami nanostructures functionalized with aptamers for specific target recognition bear attractive potential for application in targeted therapies and targeted delivery of molecular payloads.