Design and formation of the linker complex. Oligos were purchased in lyophilized form from IDT DNA. Sequences are below. LNA nucleotides are written as +C+G+A, etc. All other nucleotide are DNA. Labeling domain sequences were computer-optimized (31) to minimize sequence complementarity, homology, and melting temperature differences with programs written in MATLAB available at:http://www.dna.caltech.edu/DNAdesign/ Red linker main strand:Red linker protection strand:Blue linker main strand: 5ʼ TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATACGGGGCTGGTTA+G+G+A+T+G 3ʼBlue linker protection strand: 5ʼ TAACCAGCCCCGTAT 3ʼStrands are separately dissolved in water purified by a Milli-Q unit (Millipore) to form stock solutions at ∼300 µM. A 2 M NaCl stock solution is created and filtered using 0.22 µm filters. For the red (blue) linker complex, the main strand and the protection strand are mixed with NaCl stock solution and Milli-Q purified water to obtain 600 µL of dispersal solution with ∼ 33 µM of the main strand, ∼ 36 µM of the protection strand, and 0.1 M NaCl; the concentrations of the main and protection strands were chosen to give a 10% excess of protection strand. This solution is put in a 0.6 mL PCR tube and annealed in an Eppendorf Mastercycler from 95• C to 20• C at 1 • C per minute. The protection strand/main strand partial duplex has a melting temperature T melting ∼50• C in our buffers. Dispersal of SWNTs.To create the red (blue) NL-SWNTs, ∼1 mg of dry HiPco SWNTs are added to 400-600 µL of the dispersal solution in a 1.7 mL PCR tube. The tube is then placed in an ice-water bath and sonicated for ∼90 minutes in a Branson 2510 sonicator (100 W). The water level inside the sonication chamber and the position of the PCR tube is adjusted to apply maximum sonication power to the sample. The temperature of the water bath is maintained at ∼15• C. The SWNTs are sonicated until the solution turns a uniform gray color and all the SWNTs are completely solubilized. The solution is then centrifuged at 16,000 g for 90 min at 15• C. Following this step, the supernatant is retained while the insoluble condensate is discarded. This process yields a high concentration of well-dispersed NL-SWNTs as determined by AFM and TEM images.1

Self-assembly creates natural mineral, chemical, and biological structures of great complexity. Often, the same starting materials have the potential to form an infinite variety of distinct structures; information in a seed molecule can determine which form is grown as well as where and when. These phenomena can be exploited to program the growth of complex supramolecular structures, as demonstrated by the algorithmic self-assembly of DNA tiles. However, the lack of effective seeds has limited the reliability and yield of algorithmic crystals. Here, we present a programmable DNA origami seed that can display up to 32 distinct binding sites and demonstrate the use of seeds to nucleate three types of algorithmic crystals. In the simplest case, the starting materials are a set of tiles that can form crystalline ribbons of any width; the seed directs assembly of a chosen width with >90% yield. Increased structural diversity is obtained by using tiles that copy a binary string from layer to layer; the seed specifies the initial string and triggers growth under near-optimal conditions where the bit copying error rate is <0.2%. Increased structural complexity is achieved by using tiles that generate a binary counting pattern; the seed specifies the initial value for the counter. Self-assembly proceeds in a one-pot annealing reaction involving up to 300 DNA strands containing >17 kb of sequence information. In sum, this work demonstrates how DNA origami seeds enable the easy, high-yield, low-error-rate growth of algorithmic crystals as a route toward programmable bottom-up fabrication.DNA nanotechnology ͉ nucleation ͉ crystal growth G rowth from seeds confers both flexibility and control to a synthetic method: A single process can generate a wide range of products, with the specific choice of product determined by information contained in the seed; side products can be reduced dramatically because of the presence of a nucleation barrier, resulting in high-yield synthesis; and growth can proceed under near-ideal chemical conditions, resulting in products with few defects. Mineral and chemical compounds exhibit the simplest form of seeded growth, wherein a supersaturated solution of a polymorphic material can be inoculated with seed crystals to produce large, pure crystals of the desired form (1). In nanostructure synthesis, seeds may be used to control the diameter and crystal type of carbon nanotubes and metal nanowires (2-4). Biological organisms use information-bearing seeds with amazing control over the type, place, and timing of the structures grown from the same starting materials: Minimal media consisting of glucose, nitrogen, sulfates, and salts can be seeded with a single bacterium that will convert the starting material to biomass whose structure and composition is dictated by genomic information (5). Multicellular development, where genomic information in the zygote directs the algorithmic construction of the entire organism (6, 7), demonstrates the ultimate potential of seeded growth. Accessing this potential...

Copying and counting are useful primitive operations for computation and construction. We have made DNA crystals that copy and crystals that count as they grow. For counting, 16 oligonucleotides assemble into four DNA Wang tiles that subsequently crystallize on a polymeric nucleating scaffold strand, arranging themselves in a binary counting pattern that could serve as a template for a molecular electronic demultiplexing circuit. Although the yield of counting crystals is low, and per-tile error rates in such crystals is roughly 10%, this work demonstrates the potential of algorithmic self-assembly to create complex nanoscale patterns of technological interest. A subset of the tiles for counting form information-bearing DNA tubes that copy bit strings from layer to layer along their length.

We present a DNA nanostructure, the three-helix bundle (3HB), which consists of three double helical DNA domains connected by six immobile crossover junctions such that the helix axes are not coplanar. The 3HB motif presents a triangular cross-section with one helix lying in the groove formed by the other two. By differential programming of sticky-ends, 3HB tiles can be arrayed in two distinct lattice conformations: one-dimensional filaments and two-dimensional lattices. Filaments and lattices have been visualized by high-resolution, tapping mode atomic force microscopy (AFM) under buffer. Their dimensions are shown to be in excellent agreement with designed structures. We also demonstrate an electroless chemical deposition for fabricating metallic nanowires templated on self-assembled filaments. The metallized nanowires have diameters down to 20 nm and display Ohmic current-voltage characteristic.

Ultrathin film preparations of single-walled carbon nanotube (SWNT) allow economical utilization of nanotube properties in electronics applications. Recent advances have enabled production of micrometer scale SWNT transistors and sensors but scaling these devices down to the nanoscale, and improving the coupling of SWNTs to other nanoscale components, may require techniques that can generate a greater degree of nanoscale geometric order than has thus far been achieved. Here, we introduce linker-induced surface assembly, a new technique that uses small structured DNA linkers to assemble solution dispersed nanotubes into parallel arrays on charged surfaces. Parts of our linkers act as spacers to precisely control the internanotube separation distance down to <3 nm and can serve as scaffolds to position components such as proteins between adjacent parallel nanotubes. The resulting arrays can then be stamped onto other substrates. Our results demonstrate a new paradigm for the self-assembly of anisotropic colloidal nanomaterials into ordered structures and provide a potentially simple, low cost, and scalable route for preparation of exquisitely structured parallel SWNT films with applications in high-performance nanoscale switches, sensors, and meta-materials.

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The original version of the book was inadvertently published with the terms "undirected" and "graph" in full capitalization in Chapter 14. The erratum chapter and the book has been updated with the change.The updated online version of this chapter can be found at http://dx