The assembly of nanoparticles into three-dimensional (3D) architectures could allow for greater control of the interactions between these particles or with molecules. DNA tubes are known to form through either self-association of multi-helix DNA bundle structures or closing up of 2D DNA tile lattices. By the attachment of single-stranded DNA to gold nanoparticles, nanotubes of various 3D architectures can form, ranging in shape from stacked rings to single spirals, double spirals, and nested spirals. The nanoparticles are active elements that control the preference for specific tube conformations through size-dependent steric repulsion effects. For example, we can control the tube assembly to favor stacked-ring structures using 10-nanometer gold nanoparticles. Electron tomography revealed a left-handed chirality in the spiral tubes, double-wall tube features, and conformational transitions between tubes.Nanoparticles can exhibit distinctive electronic, magnetic, and photonic properties (1), and their assembly into well-defined one-dimensional (1D), 2D, and 3D architectures with geometric controls could add to their functionality. DNA-mediated assembly of nanoparticles is an attractive way to organize both metallic and semiconducting nanoparticles into periodic or discrete 1D and 2D structures (1-14) through the programmable base-pairing interactions and the ability to construct branched DNA nanostructures of various geometries. Recent success in using DNA as a molecular glue to direct gold nanoparticles (AuNPs) into periodic 3D crystalline lattices further demonstrates the power of DNA as building blocks for 3D nanoengineering (15,16).Here, we report a group of complex 3D geometric architectures of AuNPs created using DNA tile-mediated self-assembly. These are tubular nanostructures with various conformations and chiralities resembling those of carbon nanotubes. The nanoparticle tube assembly can be engineered both by the underlying DNA tile scaffolds and the nanoparticles themselves.

An interesting goal of nanotechnology is to assemble biomolecules to display multivalent interactions, which are characterized by simultaneous binding of multiple ligands on one biological entity to multiple receptors on another with high avidity 1 . Various approaches have been developed to engineer multivalency by linking multiple ligands together 2-4 . However, the effects of wellcontrolled inter-ligand distances on multivalency are less understood. Recent progress in selfassembling DNA tile-based nanostructures with spatial and sequence addressability 5-12 has made deterministic positioning of different molecular species possible 8,11-13 . Here we show that distancedependent multivalent binding effects can be systematically investigated by incorporating multiple affinity ligands into DNA nanostructures with precise nanometer spatial control. Using atomic force microscopy (AFM), we demonstrate direct visualization of high avidity bivalent ligands being used as pincers to capture and display protein molecules on a nanoarray. Our results set forth a path for constructing spatial combinatorics at the nanometer scale.The model system ( Fig. 1) we chose to demonstrate the distancedependent multivalent ligandprotein binding consists of two different aptamers positioned into a multi-helix DNA tile to bind a single protein target, such that the distance between them can be precisely controlled by varying the spatial arrangement of the aptamers on the DNA tile. Aptamers are oligonucleotidebased recognition regions that are selected to bind small molecules or proteins 14 . The two aptamers used here both are thrombin (a coagulation protein involved as a key promotor in blood clotting) binding aptamers which were previously selected and well characterized 15,16 . Each has a unique sequence and binds to a nearly opposite site on the thrombin molecule 15,17, 18 . Aptamer A (apt-A: 29 mer, 5′-AGT CCG TGG TAG GGC AGG TTG GGG TGA CT-3′) binds to the heparin binding exosite, 15 and aptamer B (apt-B: 15 mer, 5′-GGT TGG TGT GGT TGG-3′) binds primarily to the fibrinogen-recognition exosite. 16 It is proposed that, when these two aptamers are linked together by a rigid spacer, by varying the length of the space, an optimal inter-aptamer distance will be achieved, so that the two aptamers will act as a bivalent single molecular species that displays a stronger binding affinity to the protein than any one of the individual aptamers alone does.The multi-helix DNA tile was designed and constructed from either a fourhelix bundle (4HB) structure 19 or a five-helix bundle (5HB) structure (generated by narrowing an eight-helix bundle tile 19 ) that are modified with the closed-loop aptamer sequences extending out from (Fig. 1b). The spacing between the two aptamers can be controlled at a subnanometer precision. For example, the 5HB DNA tile can provide 2, 3.5, 5.3 and 6.9 nm inter-aptamer distances. This was accomplished by integrating apt-A into helix 1 (the left-most helix) and moving apt-B from helix 2 to 5 (to the right). Th...

Assembly of gold nanoparticles (AuNP) into designer architectures with reliablity is important for nanophotonics and nanoelectronics applications. Toward this goal we present a new strategy to prepare AuNPs monofunctionalized with lipoic acid modified DNA oligos. This strategy offers increased bonding strength between DNA oligos and AuNP surface. These conjugates are further selectively mixed with other DNA strands and assembled into fixed sized DNA nanostructures carring a discrete number of AuNPs at desired positions. Atomic force microscopy imaging reveals a dramatically improved yield of the AuNPs on DNA tile structure compared to the ensembles using monothiolate AuNP-DNA conjugates.