Supplementary Note S1: Design of DNA origamiThe program used for designing DNA origami, multishapes.m, may be downloaded from:http://www.dna.caltch.edu/SupplementaryMaterial/ Below is a description of how design proceeds using this program. It is not meant to be a manual but rather to show the level of abstraction at which the origami are designed, and to show the various types of diagrams that the program can draw to aid in design. If scaffolded DNA origami becomes widely used, a better CAD design tool will have to be written. Given a desired shape (for example the red outline in Fig. 1a) design of a DNA origami to approximate it proceeds in five phases (two manual design steps and three passes of the program):1. Generation of a block diagram. By hand, a rough geometric model is generated. It is comprised of rectangular blocks in which each block is taken to be one turn of DNA wide and one DNA helix plus the interhelix gap in height. (Such a block diagram sloppily overestimates the height of a structure by one inter-helix gap.) An example block diagram is in Supplementary Fig. S1 step 1.This step is performed with an eye towards the next step (generation of a folding path), in some cases the block diagram is conceived almost simultaneously with the folding path. The phase of the underlying periodic crossover lattice is chosen as well; generally this phasing is chosen so that seams and long edges of the shape align with columns of periodic crossovers. For blocks on the edge of the diagram, it is useful to keep track of the relationship of such blocks to the underlying crossover lattice. For an origami with 1.5-turn spacing between crossovers there are 3 possible offsets that an edge may have with respect to the underlying lattice-call them 0, +1 and -1 (Origami with 2.5 turn spacing have 5 possible offsets). For designs with a central seam, blocks on edges of offset 0 are colored red and blocks on edges of offset +1 and -1 are colored yellow and orange, depending on whether they occur to the left or right of the central seam. At this point the placement of seams may already be apparent; if so, half-blocks are used along seams. Adjacent half-blocks involved in the same scaffold crossover are colored the same (one of either green or purple) but adjacent half-blocks that participate in different crossovers are given different colors.2. Generation of a folding path, by raster fill, through the block diagram. For a given shape there are many compatible raster fill patterns; currently the raster fill pattern must be hand-designed. For any helical domain in which the scaffold is to start and end on the same side of the helix (top or bottom), an integral number of turns (blocks) is traversed. For any helical domain in which the scaffold starts and ends on opposite sides sides of the helix, the scaffold traverses an odd number of half-turns (half-blocks). An example folding path is in Supplementary Fig. S1 step 2.3. Generation of a first pass design based on the block diagram and folding path. The lengths of various heli...

Algorithms and information, fundamental to technological and biological organization, are also an essential aspect of many elementary physical phenomena, such as molecular self-assembly. Here we report the molecular realization, using two-dimensional self-assembly of DNA tiles, of a cellular automaton whose update rule computes the binary function XOR and thus fabricates a fractal pattern—a Sierpinski triangle—as it grows. To achieve this, abstract tiles were translated into DNA tiles based on double-crossover motifs. Serving as input for the computation, long single-stranded DNA molecules were used to nucleate growth of tiles into algorithmic crystals. For both of two independent molecular realizations, atomic force microscopy revealed recognizable Sierpinski triangles containing 100–200 correct tiles. Error rates during assembly appear to range from 1% to 10%. Although imperfect, the growth of Sierpinski triangles demonstrates all the necessary mechanisms for the molecular implementation of arbitrary cellular automata. This shows that engineered DNA self-assembly can be treated as a Turing-universal biomolecular system, capable of implementing any desired algorithm for computation or construction tasks.

MethodsDesign, data-processing and modelling: DNA sequences were designed using our own algorithms based on sequence symmetry minimization implemented in Matlab and C (available at http://www.dna.caltech.edu/DNAdesign/). Curve fits for persistence length data and models for lattice strain energies were calculated in Matlab.Molecular models were constructed and visualized using a combination of NAMOT, RasMol, and PyMol (scripts and coordinates at http://www.dna.caltech.edu/SupplementaryMaterial/).The molecular models are for visualization only and have not been subjected to molecular dynamics calculations.DNA sample preparation: Lyophilized HPLC-or PAGEpurified DNA oligonucleotides were purchased from Integrated DNA Technologies (Coralville, IA), resuspended in water, quantitated by UV absorbance at 260 nm, and stored at -20• C. All samples were prepared in a 1X Tris-Acetate-EDTA (TAE) buffer with 12.5 mM magnesium acetate (pH=8.3). An equimolar mixture of strands (5 strands if one tile, 10 strands if two) was annealed from 95• C to 25• C (fluorescence microscopy) steps in a PCR machine (Eppendorf Mastercycler). For AFM, each strand was present at 200 nM, for fluorescence microscopy the total concentration of tiles was kept at 400 nM. For fluorescence microscopy, a single fluorescein-labeled strand was incorporated into each tile; the position of the dye was varied from the 5 end of the #3 strand to the 5 end of the #5 strand with no apparent effect. AFM of REp+SEp(3:FAM) was similar to that of REp+SEp.Preparation of PVP coated glass: Adapted from.1 Microscope slides and coverslips were washed in 1M NaOH for 1 hour, rinsed thoroughly with de-ionized (DI) water and immersed in 1% v/v acetic acid solution for 2 hours. Then, they were rinsed again with DI water and silanized in a 1% v/v 3-(trimethoxysilyl)propylmethacrylate (Aldrich) in 1% v/v acetic acid for 36 hours. For polymer coating, 500 mL of a 4% w/v Mw = 360, 000 poly(vinylpyrrolidone) (PVP, USB Corp.) solution with 2.5 mL of 10% w/w ammonium persulfate solution and 250 µl of N,N,N ,N -tetramethylethylenediamine (TEMED, Acros) was prepared. Slides and coverslips were incubated in the PVP solution at 80• C for 18 hours. They were then rinsed and stored in DI water. Coating was stable for at least 2 weeks.Preparation for fluorescence microscopy: Samples were left overnight at room temperature after annealing. Immediately prior to use, a PVP-coated microscope slide and coverslip were rinsed with ethanol and dried. Then, 2.6 µl of solution containing DNA tubes and oxygen scavenging system (0.035 mg/ml catalase, 0.2 mg/ml glucose oxidase, 4.5 mg/ml glucose, 5% β-mercaptoethanol) was deposited onto the slide, covered with the coverslip and sealed with epoxy or parafin. The distance between slide and coverslip was ≈5 µm and the thickness of sample solution was typically narrowed to ≈3 µm by the PVP coating.Fluorescence microscopy: Samples were imaged on an inverted microscope (IX 70, Olympus) with 100X/1.40 NA oil immersion and 40X/0.75 NA air objectives. Blue lig...

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