Due to their interesting properties, research on colloidal nanocrystals has moved in the last few years from fundamental research to first applications in materials science and life sciences. In this review some recent biological applications of colloidal nanocrystals are discussed, without going into biological or chemical details. First, the properties of colloidal nanocrystals and how they can be synthesized are described. Second, the conjugation of nanocrystals with biological molecules is discussed. And third, three different biological applications are introduced: (i) the arrangement of nanocrystal-oligonucleotide conjugates using molecular scaffolds such as single-stranded DNA, (ii) the use of nanocrystal-protein conjugates as fluorescent probes for cellular imaging, and (iii) a motility assay based on the uptake of nanocrystals by living cells.

Colloidal nanocrystal/DNA conjugates hold the promise of becoming powerful probes for biological diagnostics as well as versatile building blocks for nanotechnology. To fully realize this potential, it is important to precisely control the number of oligonucleotides bound to the nanocrystal. Here we demonstrate electrophoretic isolation of 5 and 10 nm gold nanocrystals bearing discrete numbers of single-stranded DNA (1−5). The potential use of these discrete conjugates in the fabrication of novel nanostructures is discussed.

The bottom-up spatial organization of potential nanoelectronic components is a key intermediate step in the development of molecular electronics. We describe robust 3-space-spanning DNA motifs that are used to organize nanoparticles in 2D. One strand of the motif ends in a gold nanoparticle; only one DNA strand is attached to the particle. By using two of the directions of the motif to produce a two dimensional crystalline array, one direction is free to bind gold nanoparticles. Identical motifs, tailed in different sticky ends enable the 2D periodic ordering of 5 nm and 10 nm diameter gold nanoparticles. KeywordsDNA self-assembly; 2D DNA arrays; Organizing Matter with DNA; Atomic Force Microscopy; Metallic Nanoparticles; Robust DNA Motifs Metallic and semiconductor nanoparticles exhibit quantized optical and electronic properties that might be exploited in the design of future nanoelectronic devices. 1-3 However, this application requires the deliberate and precise organization of nanoparticles into specific designed structural arrangements. The control of the structure of matter on the finest possible scale entails the successful design of both stiff intramolecular motifs and robust intermolecular interactions. The specificity of DNA base-pairing has provided a 'smart-glue' approach to programming interactions between particles via hybridization of specifically designed linker strands. 4,5 Previously, stiff motifs 6 based on branched DNA have been used to produce DNA structures with a variety of patterns that are visible in the AFM; these include stripes from double crossover (DX) molecules, 7 arrays with tunable cavities from DNA parallelograms, 8 and honeycombs from DX triangles. 9 DNA-functionalized 1.4 nm gold nanoparticles have been assembled into linear arrays forming parallel stripes on a 2D DNA striped scaffolding by self-assembly during scaffolding formation 10 and 6 nm gold nanoparticles with multiple DNA attachments have been fashioned into similar arrays by in situ hybridization to a pre-assembled scaffolding on a striped DX surface. 11 Sequenceencoded in situ assembly of 5 nm and 10 nm gold particles in alternating stripes has also been achieved. 12 While such linear nanoparticle arrays are of interest for some applications, * Address correspondence to this author at ned.seeman@nyu.edu. Supporting Information Available:The sequences of the molecules used and experimental methods. This material is available free of charge via the Internet at http://pubs.acs.org/. Our experience with honeycomb lattices demonstrates that cohesion by two sticky ends on each end of a DX molecule is more robust than a single sticky end; we were unable to obtain the honeycomb arrays if only a single sticky end was used. 9 We have built several motifs that span 3-space (e.g., 6-helix bundles 15 ); one of these motifs (termed a 3D-DX triangle) is based on Mao et al.'s tensegrity triangle, 16 but contains DX molecules, instead of single helices in each of its three domains (Fig. 1). It is possible to produce 2D lat...

Thiol-modified single stranded oligonucleotides of different lengths (8 to 135 bases) were attached to the surface of 10 nm diameter Au nanocrystals with different DNA/Au ratios (1, 2, ..., saturation). The electrophoretic mobility of these conjugates was determined on 2% agarose gels, and the effective diameter of the DNA/Au conjugates was determined. This diameter depends on the conformation of the oligonucleotides adsorbed on the Au surface. For low surface coverage, nonspecific wrapping of the DNA around the nanoparticles was observed. For high surface coverage, short oligonucleotides were shown to be oriented perpendicular to the surface and fully stretched. For high surface coverage and long oligonucleotides, the inner part close to the Au surface was determined to be fully stretched and pointed perpendicular to the surface, whereas the outer part adopts random coil shape.

The development of nanoscale electronic and photonic devices will require a combination of the high throughput of lithographic patterning and the high resolution and chemical precision afforded by self-assembly. However, the incorporation of nanomaterials with dimensions of less than 10 nm into functional devices has been hindered by the disparity between their size and the 100 nm feature sizes that can be routinely generated by lithography. Biomolecules offer a bridge between the two size regimes, with sub-10 nm dimensions, synthetic flexibility and a capability for self-recognition. Here, we report the directed assembly of 5-nm gold particles into large-area, spatially ordered, two-dimensional arrays through the site-selective deposition of mesoscopic DNA origami onto lithographically patterned substrates and the precise binding of gold nanocrystals to each DNA structure. We show organization with registry both within an individual DNA template and between components on neighbouring DNA origami, expanding the generality of this method towards many types of patterns and sizes.

Artificial DNA nanostructures 1,2 show promise for the organization of functional materials 3,4 to create nanoelectronic 5 or nano-optical devices. DNA origami, in which a long single strand of DNA is folded into a shape using shorter 'staple strands' 6 , can display 6-nm-resolution patterns of binding sites, in principle allowing complex arrangements of carbon nanotubes, silicon nanowires, or quantum dots. However, DNA origami are synthesized in solution and uncontrolled deposition results in random arrangements; this makes it difficult to measure the properties of attached nanodevices or to integrate them with conventionally fabricated microcircuitry. Here we describe the use of electron-beam lithography and dry oxidative etching to create DNA origami-shaped binding sites on technologically useful materials, such as SiO 2 and diamond-like carbon. In buffer with 100 mM MgCl 2 , DNA origami bind with high selectivity and good orientation: 70-95% of sites have individual origami aligned with an angular dispersion (+ + + + +1 s.d.) as low as + + + + +108 8 8 8 8 (on diamond-like carbon) or + + + + +208 8 8 8 8 (on SiO 2 ).The semiconductor industry is currently faced with the challenges of developing lithographic technology for feature sizes below 22 nm (ref. 7) and exploring new classes of transistors that use carbon nanotubes 8 or silicon nanowires 9 . A major goal of nanotechnology is therefore to couple the self-assembly of molecular nanostructures with conventional microfabrication. A marriage of these so-called bottom-up and top-down fabrication methods would enable us to register individual molecular nanostructures, to electronically address them, and to integrate them into functional devices. One strategy is to use lithography to make templates onto which discrete components can self-assemble. Examples include the assembly of nanoparticles 10,11 , carbon nanotubes 12,13 and nanowires 14 . Lithographic templates can also be used to create hierarchical order: the nanostructures they organize can themselves have internal features with dimensions significantly smaller than those of the original template 15 and can serve as scaffolds for the assembly of still smaller components.Artificial DNA nanostructures are well suited to this approach. They can be synthesized with attachment groups (such as biotin or single-stranded DNA hooks) at defined locations, which can bind objects such as gold nanoparticles 4,16 . Easily designed in arbitrary shapes, DNA origami typically carry 200 such independently addressable sites at a resolution of 6 nm. Figure 1a depicts the self-assembly of triangular DNA origami in solution (see Supplementary Methods 1) and shows an atomic force micrograph (AFM) of their random deposition on mica, a technique ill-suited for integration with microfabrication. Previous lithographically patterned deposition of organic compounds 17 , single-and doublestranded DNA molecules [18][19][20] or DNA nanostructures 21 has achieved highly selective adsorption, but the molecules were smaller than the lith...

Water-soluble, highly fluorescent, silanized semiconductor nanocrystals with different surface charges were synthesized. To covalently attach the nanocrystals to biological macromolecules with a variety of mild coupling chemistries, the outermost siloxane shells were derivatized with thiol, amino, or carboxyl functional groups. Single-or double-stranded DNA was coupled to the nanocrystal surfaces by using commercially available bifunctional cross-linker. Conjugation had little effect on the optical properties of the nanocrystals, and the resulting conjugates were more stable than previously reported systems. By using the strategies developed in this study, most biomolecules can be covalently coupled to semiconductor nanocrystals. These nanocrystal-DNA conjugates promise to be a versatile tool for fluorescence imaging and probing of biological systems.

Discrete Au nanoparticle/DNA conjugates have been isolated by electrophoresis and used to form small groupings of particles, such as dimers and trimers. The use of purified conjugates leads to a higher yield of the target structure, and it has allowed us better control and understanding of the system. Newly accessible questions, such as the electrophoretic mobility of nanoparticle/DNA hybrids and the critical role of particle surface charge on mobility have been studied. Detailed characterization by Transmission Electron Microscopy (TEM) has now been done due to the higher quality of the samples.A computer program to generate pair distribution functions from TEM images was developed, pointing out the dependence of interparticle distance with DNA length on dimers of particles.2