Optimal Tile-Based DNA Self-Assembly Designs for Lattice Graphs and Platonic Solids (original) (raw)

Computational complexity and pragmatic solutions for flexible tile based DNA self-assembly

2021

Branched junction molecule assembly of DNA nanostructures, pioneered by Seeman’s laboratory in the 1980s, has become increasingly sophisticated, as have the assembly targets. A critical design step is finding minimal sets of branched junction molecules that will self-assemble into target structures without unwanted substructures forming. We use graph theory, which is a natural design tool for self-assembling DNA complexes, to address this problem. After determining that finding optimal design strategies for this method is generally NP-complete, we provide pragmatic solutions in the form of programs for special settings and provably optimal solutions for natural assembly targets such as platonic solids, regular lattices, and nanotubes. These examples also illustrate the range of design challenges.

Self-Assembly of Irregular Graphs Whose Edges Are DNA Helix Axes

Journal of The American Chemical Society, 2004

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.

Self-assembly with Geometric Tiles

Lecture Notes in Computer Science, 2012

In this work we propose a generalization of Winfree's abstract Tile Assembly Model (aTAM) in which tile types are assigned rigid shapes, or geometries, along each tile face. We examine the number of distinct tile types needed to assemble shapes within this model, the temperature required for efficient assembly, and the problem of designing compact geometric faces to meet given compatibility specifications. Our results show a dramatic decrease in the number of tile types needed to assemble n×n squares to Θ( √ log n) at temperature 1 for the most simple model which meets a lower bound from Kolmogorov complexity, and O(log log n) in a model in which tile aggregates must move together through obstacle free paths within the plane. This stands in contrast to the Θ(log n/ log log n) tile types at temperature 2 needed in the basic aTAM. We also provide a general method for simulating a large and computationally universal class of temperature 2 aTAM systems with geometric tiles at temperature 1. Finally, we consider the problem of computing a set of compact geometric faces for a tile system to implement a given set of compatibility specifications. We show a number of bounds on the complexity of geometry size needed for various classes of compatibility specifications, many of which we directly apply to our tile assembly results to achieve non-trivial reductions in geometry size.

Combinatorial optimization problems in self-assembly

2002

Self-assembly is the ubiquitous process by which simple objects autonomously assemble into intricate complexes. It has been suggested that intricate self-assembly processes will ultimately be used in circuit fabrication, nano-robotics, DNA computation, and amorphous computing. In this paper, we study two combinatorial optimization problems related to efficient self-assembly of shapes in the Tile Assembly Model of self-assembly proposed by Rothemund and Winfree . The first is the Minimum Tile Set Problem, where the goal is to find the smallest tile system that uniquely produces a given shape. The second is the Tile Concentrations Problem, where the goal is to decide on the relative concentrations of different types of tiles so that a tile system assembles as quickly as possible. The first problem is akin to finding optimum program size, and the second to finding optimum running time for a "program" to assemble the shape.

Computation by Self-assembly of DNA Graphs

Genetic Programming and Evolvable Machines, 2003

Using three dimensional graph structure and DNA self-assembly we show that theoretically 3-SAT and 3-colorability can be solved in a constant number of laboratory steps. In this assembly, junction molecules and duplex DNA molecules are the basic building blocks. The graphs involved are not necessarily regular, so experimental results of self-assembling non regular graphs using junction molecules as vertices and duplex DNA molecules as edge connections are presented.

Some structural properties of planar graphs and their applications to 3-choosability

Discrete Mathematics, 2012

In this article, we consider planar graphs in which each vertex is not incident to some cycles of given lengths, but all vertices can have different restrictions. This generalizes the approach based on forbidden cycles which corresponds to the case where all vertices have the same restrictions on the incident cycles. We prove that a planar graph G is 3-choosable if it is satisfied one of the following conditions: (1) each vertex x is neither incident to cycles of lengths 4, 9, ix with ix ∈ {5, 7, 8}, nor incident to 6-cycles adjacent to a 3-cycle. (2) each vertex x is not incident to cycles of lengths 4, 7, 9, ix with ix ∈ {5, 6, 8}. This work implies five results already published [13, 3, 7, 12, 4].

Hexagonal tilings and Locally C6 graphs

2005

We give a complete classification of hexagonal tilings and locally C6 graphs, by showing that each of them has a natural embedding in the torus or in the Klein bottle (see [12]). We also show that locally grid graphs, defined in [9, 12], are minors of hexagonal tilings (and by duality of locally C6 graphs) by contraction of a particular perfect matching and deletion of the resulting parallel edges, in a form suitable for the study of their Tutte uniqueness.

Synthesizing Minimal Tile Sets for Patterned DNA Self-assembly

Lecture Notes in Computer Science, 2011

The Pattern self-Assembly Tile set Synthesis (PATS) problem is to determine a set of coloured tiles that self-assemble to implement a given rectangular colour pattern. We give an exhaustive branch-and-bound algorithm to find tile sets of minimum cardinality for the PATS problem. Our algorithm makes use of a search tree in the lattice of partitions of the ambient rectangular grid, and an efficient bounding function to prune this search tree. Empirical data on the performance of the algorithm shows that it compares favourably to previously presented heuristic solutions to the problem.