The representation shown illustrates the input corresponding to 10101 binary (21 decimal). == (b) Computation == We have implemented the computational model by tiles that are triple crossover (TX) DNA molecules; these contain three double helical domains in a roughly Rabbit Polyclonal to RTCD1 planar arrangement. of these TX tiles contains sticky ends that also correspond to 0 or 1. Two different DNA tiles can chelate these output domains: A 5 nm gold nanoparticle is attached to the chelating tile that binds to 0-domains and a 10 nm gold nanoparticle is attached to the chelating tile that binds to 1-domains. The answer to the division is represented by the series of gold nanoparticles, which can be interpreted as a binary number. The answers of the computation are read out by examination of the transducer complexes under a transmission electron microscope. The start or end points of the output sequence can be indicated by the presence of a 15 nm gold nanoparticle. This work demonstrates two previously unreported features integrated in a single framework: [1] a system that combines DNA algorithmic self-assembly with DNA nanomechanical devices that control that input, and [2] the arrangement of non-DNA species, here metallic nanoparticles, through DNA algorithmic self-assembly. The nanomechanical devices are controlled by single-stranded DNA strands, allowing multiple input sequences to be applied to the rest of the system, thus guiding the algorithmic self-assembly to a variety of outputs. == Introduction == A collection of synthetic DNA molecules have been designed and shown to assemble into branched motifs,14as well as more complex species that entail the lateral fusion of DNA double helices.5The second group of motifs includes double crossover (DX) molecules,6triple crossover (TX) molecules7and paranemic crossover (PX) molecules.8,9Double10and triple7crossover molecules have been used as tiles and building blocks for nanoscale 2D arrays, and tensegrity triangles11have been used to produce macroscopic 3D crystals.12 It can be shown that two dimensional arrays made from DX or TX DNA motifs can simulate the dynamics of a bounded one dimensional cellular automaton and therefore are capable of performing computation as a Universal Turing Machine.13Successful experiments have confirmed the possibility of computation by DNA self-assembly: binary addition (simulation of a cumulative exclusive OR (called XOR)) using ON-013100 triple crossover molecules14as well as aperiodic Sierpinski triangle assembly by DX molecules have been reported.15Although not explicitly mentioned, both of these algorithmic assemblies could be viewed as finite state automata simulations. Further simulations of finite state automata that use duplex DNA molecules and a restriction endonuclease have been reported by Shapiro, Keinan, Benenson and their colleagues.16,17 In addition to these self-assemblies, a variety of sequence-dependent DNA nanomechanical devices have been reported, including 2-state devices,18,19a 3-state device,20track-based walkers,2124and a combination of devices with a walker that performs the functions of an assembly line.25These systems all depend on the use of toehold-based fuel strands that unset the state of a device ON-013100 by removing a strand from it isothermally.18The PX-JX2device19has two distinct states and each is obtained by the addition of two DNA strands that hybridize with it, so that the molecule is in either of two states, termed the PX state or the JX2state. The two states differ from each other in that one end is rotated relative to the other by a half-turn. A group of these devices can be addressed individually, 26so that different devices can act simultaneously, but independently.27 It is well known that ON-013100 by iteration of generalized sequential machines (finite state machines mapping symbols into strings) all computable functions can be iterated.28,29The full computational power depends on the possibility of iterating the finite state machines. Wang tiles30can simulate iterated transducers and recursive (computable) functions. Wang tiles consist of a set of tiles (usually square) with colored edges; the tiles self-assemble according to the local rule requiring edges with the same color to pair with each other; this type of self-assembly has been shown to simulate a Turing machine, a universal computer.30Both the XOR simulation14and the Sierpinski triangle assembly15can be seen as DNA Wang tile assemblies. Here, we have developed this idea further and we report the use of PX-JX2devices to assemble the input.