DNA Triangles and Self-Assembled Hexagonal Tilings

Chelyapov, N. V.; Brun, Yuriy; Gopalkrishnan, Manoj; Reishus, Dustin; Shaw, Bilal; Adleman, Leonard M.

doi:10.1021/ja0458120

Cited by 120 publications

(94 citation statements)

References 11 publications

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“…Once suitably rigid motifs were developed, it was possible to build 2D arrays with programmable features [4][5][6][7][8][9][10]. The original impetus for building arrays came from the hope of improving macromolecular crystallization [1], but early goals also included organizing nanoelectronics [11], and DNAbased computation [12].…”

Section: Introductionmentioning

confidence: 99%

From genes to machines: DNA nanomechanical devices

Seeman

2005

Trends in Biochemical Sciences

340

213

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The structural properties that enable DNA to serve so effectively as genetic material can also be utilized for other purposes. The complementarity that leads to the pairing of the strands of the DNA double helix can be exploited to assemble more complex motifs, based on branched structures. These structures have been used as the basis of larger constructions in 2D and 3D. In addition, they have been used to make nanomechanical devices. These devices range from DNAbased shape-shifting structures to gears and walkers, a DNA stress-gauge, and even a translation device. The devices are activated by mechanisms as diverse as small molecules, proteins, and, most intriguingly, other molecules of DNA.

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Section: Introductionmentioning

confidence: 99%

From genes to machines: DNA nanomechanical devices

Seeman

2005

Trends in Biochemical Sciences

340

213

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“…The self-assembly of DNA tiles can be used both as a powerful computational mechanism [8,13,21,24,27] and as a bottom-up nanofabrication technique [18]. Periodic 2D DNA lattices have been successfully constructed with a variety of DNA tiles, for example, double-crossover (DX) DNA tiles [26], rhombus tiles [12], triplecrossover (TX) tiles [7], "4x4" tiles [30], triangle tiles [9], and hexagonal tiles [3]. Aperiodic barcode DNA lattices have also been experimentally constructed [29].…”

Section: Introductionmentioning

confidence: 99%

Compact Error-Resilient Computational DNA Tiling Assemblies

2005

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Abstract. The self-assembly process for bottom-up construction of nanostructures is of key importance to the emerging scientific discipline Nanoscience. However, algorithmic self-assembly at the molecular scale is prone to a quite high rate of error. Such high error rate is a major barrier to large-scale experimental implementation of algorithmic DNA tilings. The goals of this paper are to develop theoretical methods for compact error-resilient algorithmic DNA tilings and to analyze these methods by thermodynamic analysis and computer simulation. Prior work by Winfree provided an innovative approach to decrease tiling self-assembly mismatch errors without decreasing the intrinsic error rate £ of assembling a single tile. However, his technique resulted in a final structure larger than the original one (four times larger for decreasing the error to £ ¥ ¤ , nine times for to £ § ¦). In this paper, we describe various compact error-resilient tiling methods that do not increase the size of the tiling assembly. These methods apply to the assembly of Boolean arrays which perform input sensitive computations (among other computations). Our 2-way (3-way) overlay redundancy construction decreases the error rate from, without increasing the size of the assembly. As in Winfree's constructions, the number of distinct tile types required is also increased in our error-resilient tiling constructions. These results were further validated using computer simulation.

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“…Figure 1 (b) illustrates one example rule set for the cellular automaton shown in Figure 1 (a). The rule set consists of 8 transition rules (numbered (1) - (8) in the figure). For example, according to rule (1), if the current cell and both of its neighbors have color BLACK, at next time step, the middle cell will change to color WHITE.…”

Section: Introductionmentioning

confidence: 99%

Design of Autonomous DNA Cellular Automata

Yin

Sahu

Turberfield

et al. 2006

Lecture Notes in Computer Science

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Abstract. Recent experimental progress in DNA lattice construction, DNA robotics, and DNA computing provides the basis for designing DNA cellular computing devices, i.e. autonomous nano-mechanical DNA computing devices embedded in DNA lattices. Once assembled, DNA cellular computing devices can serve as reusable, compact computing devices that perform (universal) computation, and programmable robotics devices that demonstrate complex motion. As a prototype of such devices, we recently reported the design of an Autonomous DNA Turing Machine, which is capable of universal sequential computation, and universal translational motion, i.e. the motion of the head of a single tape universal mechanical Turing machine. In this paper, we describe the design of an Autonomous DNA Cellular Automaton (ADCA), which can perform parallel universal computation by mimicking a one-dimensional (1D) universal cellular automaton. In the computation process, this device, embedded in a 1D DNA lattice, also demonstrates well coordinated parallel motion. The key technical innovation here is a molecular mechanism that synchronizes pipelined "molecular reaction waves" along a 1D track, and in doing so, realizes parallel computation. We first describe the design of ADCA on an abstract level, and then present detailed DNA sequence level implementation using commercially available protein enzymes. We also discuss how to extend the 1D design to 2D.

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DNA Triangles and Self-Assembled Hexagonal Tilings

Cited by 120 publications

References 11 publications

From genes to machines: DNA nanomechanical devices

From genes to machines: DNA nanomechanical devices

Compact Error-Resilient Computational DNA Tiling Assemblies

Design of Autonomous DNA Cellular Automata

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