A DNA nanostructure consisting of four four-arm junctions oriented with a square aspect ratio was designed and constructed. Programmable self-assembly of 4 x 4 tiles resulted in two distinct lattice morphologies: uniform-width nanoribbons and two-dimensional nanogrids, which both display periodic square cavities. Periodic protein arrays were achieved by templated self-assembly of streptavidin onto the DNA nanogrids containing biotinylated oligonucleotides. On the basis of a two-step metallization procedure, the 4 x 4 nanoribbons acted as an excellent scaffold for the production of highly conductive, uniform-width, silver nanowires.

This paper extends the study and prototyping of unusual DNA motifs, unknown in nature, but founded on principles derived from biological structures. Artificially designed DNA complexes show promise as building blocks for the construction of useful nanoscale structures, devices, and computers. The DNA triple crossover (TX) complex described here extends the set of experimentally characterized building blocks. It consists of four oligonucleotides hybridized to form three double-stranded DNA helices lying in a plane and linked by strand exchange at four immobile crossover points. The topology selected for this TX molecule allows for the presence of reporter strands along the molecular diagonal that can be used to relate the inputs and outputs of DNA-based computation. Nucleotide sequence design for the synthetic strands was assisted by the application of algorithms that minimize possible alternative base-pairing structures. Synthetic oligonucleotides were purified, stoichiometric mixtures were annealed by slow cooling, and the resulting DNA structures were analyzed by nondenaturing gel electrophoresis and heat-induced unfolding. Ferguson analysis and hydroxyl radical autofootprinting provide strong evidence for the assembly of the strands to the target TX structure. Ligation of reporter strands has been demonstrated with this motif, as well as the self-assembly of hydrogen-bonded two-dimensional crystals in two different arrangements. Future applications of TX units include the construction of larger structures from multiple TX units, and DNA-based computation. In addition to the presence of reporter strands, potential advantages of TX units over other DNA structures include space for gaps in molecular arrays, larger spatial displacements in nanodevices, and the incorporation of well-structured out-of-plane components in two-dimensional arrays.

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Recent work has demonstrated the self-assembly of designed periodic two-dimensional arrays composed of DNA tiles, in which the intermolecular contacts are directed by 'sticky' ends. In a mathematical context, aperiodic mosaics may be formed by the self-assembly of 'Wang' tiles, a process that emulates the operation of a Turing machine. Macroscopic self-assembly has been used to perform computations; there is also a logical equivalence between DNA sticky ends and Wang tile edges. This suggests that the self-assembly of DNA-based tiles could be used to perform DNA-based computation. Algorithmic aperiodic self-assembly requires greater fidelity than periodic self-assembly, because correct tiles must compete with partially correct tiles. Here we report a one-dimensional algorithmic self-assembly of DNA triple-crossover molecules that can be used to execute four steps of a logical (cumulative XOR) operation on a string of binary bits.

DNA sequence design. DNA sequences for 3-, 4-, 5-, and 6-helix ribbon systems, and 4-, 5-, and 6-helix tube systems were designed and optimized using the SEQUIN software (S1) and the TileSoft software (S2) to minimize sequence symmetry (S1). The other systems were designed using an unpublished sequence design component of the NUPACK server (www.nupack.org) to maximize the affinity and specificity for the target structures (S3). Sometimes, manual optimization was further performed on selected regions. Sample preparation. DNA strands were synthesized by Integrated DNA Technology, Inc. (www.idtdna.com) and purified by denaturing polyacrylamide gel electrophoresis or HPLC. The concentrations of the DNA strands were determined by the measurement of ultraviolet absorption at 260 nm. To assemble the structures, DNA strands were mixed stoichiometrically to a final concentration of ∼1 μM for 20-helix ribbons and 20-helix tubes and ∼3 μM for other structures in 1× TAE/Mg ++ buffer (20 mM Tris, pH 7.6, 2 mM EDTA, 12.5 mM MgCl 2) and annealed in a water bath in a styrofoam box by cooling from 90 • C to 23 • C over a period of 24 to 72 hours. AFM imaging. AFM images were obtained using an MultiMode SPM with a Nanoscope IIIa controller (Veeco, Santa Barbara, CA) equipped with an Analog Q-control to optimize the sensitivity of the tapping mode (nanoAnalytics GmbH, Münster, Germany). A ∼40 μL drop of 1× TAE/Mg ++ followed by a ∼5 μL drop of annealed sample was applied onto the surface of a freshly cleaved mica and left for approximately 2 minutes. Sometimes, additional dilution of the sample was performed to achieve the desired sample density. On a few occasions, supplemental 1× TAE/8mM Ni ++ was added to increase the strength of DNA-mica binding (S4). Before placing the fluid cell on top of the mica puck, an additional ∼20 μL of 1× TAE/Mg ++ buffer was added to the cavity between the fluid cell and the AFM cantilever chip to avoid bubbles. The AFM tips used were either the short and thin cantilever in the DNP-S oxide sharpened silicon nitride cantilever chip (Veeco Probes, Camarillo, CA) or the short cantilever in the SiNi chip (BudgetSensors, Sofia, Bulgaria). Fluorescence imaging and length measurements. For fluorescence microscopy imaging, the 5-end of the U1 strand was labeled with a Cy3 fluorophore. A 4 μL drop of 10 nM SST sample was deposited onto an untreated coverslip. The light microscope is a home-built prism-based TIRF microscope. The samples were excited with 532 nm solid-state laser (CrystaLaser, Reno, NV). The Cy3 emission was detected by a 60×, 1.2 NA water immersion objective (Nikon), a Dual-View 2-channel filter cube (Photometrics, Pleasanton, CA), and a C9100-02 electron multiplier CCD camera (Hamamatsu). The images were analyzed using the imageJ image processing software (NIH) and MATLAB. A threshold was applied to each image to differentiate the nanotubes and the glass surface. The "skeletonize" command in imageJ is used to reduce a tube image to a single pixel wide skeleton, and the length of the skeleton ...

Recent years have witnessed substantial advances in the use of DNA as a smart material to construct periodically patterned structures. 1 DNA also has been designed to direct the assembly of other functional molecules by the use of appropriate attachment chemistries. 2 The diversity of materials which can be chemically attached to DNA considerably enhances the attractiveness of DNA nanostructures for assembly of other materials. Self-assembling DNA tiling lattices represent a versatile system for nanoscale construction. The methodology of DNA lattice self-assembly begins with the chemical synthesis of single-stranded DNA molecules, which self-assemble into DNA branched motif complexes, known as tiles. 1b-1f DNA tiles can carry sticky-ends that preferentially match the sticky-ends of other particular DNA tiles, thereby facilitating the further assembly into lattices. Self-assembled twodimensional DNA tiling lattices composed of tens of thousands of tiles have been demonstrated. 1b-1f Self-assembled DNA arrays provide an excellent template for spatially positioning other molecules with increased relative precision and programmability.Here we report an experiment using a linear array of DNA triple crossover molecules (TX) to controllably template the self-assembly of two forms (single-layer or double-layer) of streptavidin linear arrays through biotin-streptavidin interaction. Figure 1 illustrates the design. The TX molecule used here was derived from the DNA motif described elsewhere, 1c and it consists of seven oligonucleotides hybridized to form three double-stranded helices lying in a plane and linked by strand exchange at four immobile crossover points. The TX molecule shown in Figure 1a is designed such that it contains two stem loops protruding, one each out of the upper and the lower helices. A linear array of the TX molecules can be obtained by designing three pairs of sticky ends where their complementarity is represented by matching color and geometric shape ( Figure 1b). To template the assembly of streptavidin molecules, the hairpin loops were modified to incorporate two biotin groups per loop, indicated by the small blue dots. Formation of single-layer or double-layer streptavidin linear arrays was controlled using two different templates which are illustrated in Figure 1b. In the first template (left panel), only one stem loop in each TX molecule was modified with biotin groups. However, in the second template (right panel), both stem loops were modified to incorporate biotins. The binding of streptavidin molecules, which is represented as yellow dots, to the two different templates resulted in singlelayer or double-layer streptavidin linear arrays, as shown in Figure 1b.Streptavidin has a diameter of ∼4 nm. Its binding to the selfassembled TX array generates bumps at biotinylated locations on hairpin loops of the TX tiles which can be detected by atomic force microscopy imaging (AFM). Figure 2a shows an AFM image of a sample containing only streptavidin, demonstrating that the streptavidin molecule...

The programmed self-assembly of patterned aperiodic molecular structures is a major challenge in nanotechnology and has numerous potential applications for nanofabrication of complex structures and useful devices. Here we report the construction of an aperiodic patterned DNA lattice (barcode lattice) by a selfassembly process of directed nucleation of DNA tiles around a scaffold DNA strand. The input DNA scaffold strand, constructed by ligation of shorter synthetic oligonucleotides, provides layers of the DNA lattice with barcode patterning information represented by the presence or absence of DNA hairpin loops protruding out of the lattice plane. Self-assembly of multiple DNA tiles around the scaffold strand was shown to result in a patterned lattice containing barcode information of 01101. We have also demonstrated the reprogramming of the system to another patterning. An inverted barcode pattern of 10010 was achieved by modifying the scaffold strands and one of the strands composing each tile. A ribbon lattice, consisting of repetitions of the barcode pattern with expected periodicity, was also constructed by the addition of sticky ends. The patterning of both classes of lattices was clearly observable via atomic force microscopy. These results represent a step toward implementation of a visual readout system capable of converting information encoded on a 1D DNA strand into a 2D form readable by advanced microscopic techniques. A functioning visual output method would not only increase the readout speed of DNA-based computers, but may also find use in other sequence identification techniques such as mutation or allele mapping.T he field of nanotechnology holds tremendous promise. If the molecular and supramolecular world can be controlled at will, then it may be possible to achieve vastly better performance for computers and memories, and it might open up a host of other applications in materials science, medicine, and biology. Because of this promise, numerous research teams have embarked on the development of various detailed aspects of nanotechnology, such as the use of physically strong and electrically active fullerene materials (1), and organic molecules that have electrical switching properties (2). The construction of molecular-scale structures is one of the key challenges facing science and technology in the 21st century. There are two distinct approaches to the fabrication of nanomaterials: top-down methods and bottom-up approaches. Topdown methods, exemplified by e-beam lithography, may be limited by their serial nature, whereas bottom-up methods using self-assembly are by nature highly parallel. Although self-assembly methods are well known and have been long used by chemists, they conventionally result in structures with limited complexity (e.g., regular, periodic patterning with a small number of programmed association rules), and most current methods do not allow the self-assembly to be readily reprogrammable.In recent years, DNA has been advanced as a useful material for constructing periodica...

We demonstrate the precise control of periodic spacing between individual protein molecules by programming the self-assembly of DNA tile templates. In particular, we report the application of two self-assembled periodic DNA structures, two-dimensional nanogrids, and one-dimensional nanotrack, as template for programmable self-assembly of streptavidin protein arrays with controlled density.