Implementing Logic Gates by DNA Crystal Engineering.

DNA self-assembly computation is attractive for its potential to perform massively parallel information processing at the molecular level while at the same time maintaining its natural biocompatibility. It has been extensively studied at the individual molecule level, but not as much as ensembles in 3D. Here, the feasibility of implementing logic gates, the basic computation operations, in large ensembles: macroscopic, engineered 3D DNA crystals is demonstrated. The building blocks are the recently developed DNA double crossover-like (DXL) motifs. They can associate with each other via sticky-end cohesion. Common logic gates are realized by encoding the inputs within the sticky ends of the motifs. The outputs are demonstrated through the formation of macroscopic crystals that can be easily observed. This study points to a new direction of construction of complex 3D crystal architectures and DNA-based biosensors with easy readouts.

Programming DNA Self-Assembly by Geometry†.

This manuscript introduces geometry as a means to program the tile-based DNA self-assembly in two and three dimensions. This strategy complements the sequence-focused programmable assembly. DNA crystal assembly critically relies on intermotif, sticky-end cohesion, which requires complementarity not only in sequence but also in geometry. For DNA motifs to assemble into crystals, they must be associated with each other in the proper geometry and orientation to ensure that geometric hindrance does not prevent sticky ends from associating. For DNA motifs with exactly the same pair of sticky-end sequences, by adjusting the length (thus, helical twisting phase) of the motif branches, it is possible to program the assembly of these distinct motifs to either mix with one another, to self-sort and consequently separate from one another, or to be alternatingly arranged. We demonstrate the ability to program homogeneous crystals, DNA "alloy" crystals, and definable grain boundaries through self-assembly. We believe that the integration of this strategy and conventional sequence-focused assembly strategy could further expand the programming versatility of DNA self-assembly.

Paranemic Crossover DNA: There and Back Again.

Over the past 35 years, DNA has been used to produce various nanometer-scale constructs, nanomechanical devices, and walkers. Construction of complex DNA nanostructures relies on the creation of rigid DNA motifs. Paranemic crossover (PX) DNA is one such motif that has played many roles in DNA nanotechnology. Specifically, PX cohesion has been used to connect topologically closed molecules, to assemble a three-dimensional object, and to create two-dimensional DNA crystals. Additionally, a sequence-dependent nanodevice based on conformational change between PX and its topoisomer, JX2, has been used in robust nanoscale assembly lines, as a key component in a DNA transducer, and to dictate polymer assembly. Furthermore, the PX motif has recently found a new role directly in basic biology, by possibly serving as the molecular structure for double-stranded DNA homology recognition, a prominent feature of molecular biology and essential for many crucial biological processes. This review discusses the many attributes and usages of PX-DNA-its design, characteristics, applications, and potential biological relevance-and aims to accelerate the understanding of PX-DNA motif in its many roles and manifestations.

A Signal-Passing DNA-Strand-Exchange Mechanism for Active Self-Assembly of DNA Nanostructures.

DNA nanostructured tiles play an active role in their own self-assembly in the system described herein whereby they initiate a binding event that produces a cascading assembly process. We present DNA tiles that have a simple but powerful property: they respond to a binding event at one end of the tile by passing a signal across the tile to activate a binding site at the other end. This action allows sequential, virtually irreversible self-assembly of tiles and enables local communication during the self-assembly process. This localized signal-passing mechanism provides a new element of control for autonomous self-assembly of DNA nanostructures.

Biologically relevant molecular transducer with increased computing power and iterative abilities.

As computing devices, which process data and interconvert information, transducers can encode new information and use their output for subsequent computing, offering high computational power that may be equivalent to a universal Turing machine. We report on an experimental DNA-based molecular transducer that computes iteratively and produces biologically relevant outputs. As a proof of concept, the transducer accomplished division of numbers by 3. The iterative power was demonstrated by a recursive application on an obtained output. This device reads plasmids as input and processes the information according to a predetermined algorithm, which is represented by molecular software. The device writes new information on the plasmid using hardware that comprises DNA-manipulating enzymes. The computation produces dual output: a quotient, represented by newly encoded DNA, and a remainder, represented by E. coli phenotypes. This device algorithmically manipulates genetic codes.

A Programmable Transducer Self-Assembled from DNA.

A transducer consists of an input/output alphabet, a finite set of states, and a transition function. From an input symbol applied to a given state, the transition function determines the next state, and an output symbol. Using DNA, we have constructed a transducer that divides a number by 3. The input consists of a series of individually addressable 2-state DNA nanomechanical devices that control the orientations of a group of flat 6-helix DNA motifs; these motifs have edge domains tailed in sticky ends corresponding to the numbers 0 and 1. Three-domain DNA molecules (TX tiles) act as computational tiles that correspond to the transitions that the transducer can undergo. The output domain 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.

Construction of a DNA nano-object directly demonstrates computation.

We demonstrate a computing method in which a DNA nano-object representing the solution of a problem emerges as a result of self-assembly. We report an experiment in which three-vertex colorability for a six-vertex graph with nine edges is solved by constructing a DNA molecule representing the colored graph itself. Our findings show that computation based on "shape processing" is a viable alternative to symbol processing when computing by molecular self-assembly.

Reciprocal DNA nanomechanical devices controlled by the same set strands.

Reciprocating devices are key features in macroscopic machines. We have adapted the DNA PX-JX(2) device to a reciprocal format. The PX-JX(2) device is a robust sequence-dependent nanomachine, whose state is established by a pair of control strands that set it to be either in the PX state or in the JX(2) state. The two states differ by a half-turn rotation between their ends. Here we report the construction of a pair of reciprocal PX-JX(2) devices, wherein the control strands leading to the PX state in one device lead to the JX(2) state in the other device and vice versa. The formation, transformation, and reciprocal motions of these two device systems are confirmed using gel electrophoresis and atomic force microscopy. This system is likely to be of use for molecular robotic applications where reciprocal motions are of value in addition its inherent contribution to molecular choreography and molecular aesthetics.

Self-assembly of irregular graphs whose edges are DNA helix axes.

A variety of computational models have been introduced recently that are based on the properties of DNA. In particular, branched junction molecules and graphlike DNA structures have been proposed as computational devices, although such models have yet to be confirmed experimentally. DNA branched junction molecules have been used previously to form graph-like three-dimensional DNA structures, such as a cube and a truncated octahedron, but these DNA constructs represent regular graphs, where the connectivities of all of the vertexes are the same. Here, we demonstrate the construction of an irregular DNA graph structure by a single step of self-assembly. A graph made of five vertexes and eight edges was chosen for this experiment. DNA branched junction molecules represent the vertexes, and duplex molecules represent the edges; in contrast to previous work, specific edge molecules are included as components. We demonstrate that the product is a closed cyclic single-stranded molecule that corresponds to a double cover of the graph and that the DNA double helix axes represent the designed graph. The correct assembly of the target molecule has been demonstrated unambiguously by restriction analysis.