Self-assembly Of DNA Tiles Research Articles

Guided Self-Assembly of DNA Tiles into One- and Two-Dimensional Patterns Using Strand-Displacement and Optochemical Pathways

Guided Self-Assembly of DNA Tiles into One- and Two-Dimensional Patterns Using Strand-Displacement and Optochemical Pathways

Size-Controlled DNA Tile Self-Assembly Nanostructures Through Caveolae-Mediated Endocytosis for Signal-Amplified Imaging of MicroRNAs in Living Cells.

Signal-amplified imaging of microRNAs (miRNAs) is a promising strategy at the single-cell level because liquid biopsy fails to reflect real-time dynamic miRNA levels. However, the internalization pathways for available conventional vectors predominantly involve endo-lysosomes, showing nonideal cytoplasmic delivery efficiency. In this study, size-controlled 9-tile nanoarrays are designed and constructed by integrating catalytic hairpin assembly (CHA) with DNA tile self-assembly technology to achieve caveolae-mediated endocytosis for the amplified imaging of miRNAs in a complex intracellular environment. Compared with classical CHA, the 9-tile nanoarrays possess high sensitivity and specificity for miRNAs, achieve excellent internalization efficiency by caveolar endocytosis, bypassing lysosomal traps, and exhibit more powerful signal-amplified imaging of intracellular miRNAs. Because of their excellent safety, physiological stability, and highly efficient cytoplasmic delivery, the 9-tile nanoarrays can realize real-time amplified monitoring of miRNAs in various tumor and identical cells of different periods, and imaging effects are consistent with the actual expression levels of miRNAs, ultimately demonstrating their feasibility and capacity. This strategy provides a high-potential delivery pathway for cell imaging and targeted delivery, simultaneously offering a meaningful reference for the application of DNA tile self-assembly technology in relevant fundamental research and medical diagnostics.

Self-Assembly of DNA Tiles with G-Quadruplex DNAzyme Catalytic Activity for Sensing Applications.

DNA tiles form through self-assembly of a small number of DNA strands that interact through basic repeated interactions, allowing the growth of nanoscale structures seeded by molecular inputs. If an approach for catalytic signal amplification can be integrated into the resultant nanostructure, then one can anticipate biosensing or diagnostic applications mediated by DNA tile self-assembly. Here, two-dimensional DNA tiles with split quadruplexes were designed as diagnostic tools for nucleic acid sensing without the use of protein enzymes. The presence of a target sequence leads to formation of extended microscale structures with arrayed multiple G-quadruplexes across the tile plane, with catalytic activity coupled to a colorimetric reporter. Such a mechanism has potential for low-cost signal amplification using unmodified DNA without the use of protein enzymes for biosensing.

Tomography of DNA tiles influences the kinetics of surface-mediated DNA self-assembly

This manuscript studies the impact of extruding hairpins on two-dimensional self-assembly of DNA tiles on solid surface. Hairpins are commonly used as tomographic markers in DNA nanostructures for atomic force microscopy imaging. In this study, we have discovered that hairpins play a more active role. They modulate the adsorption of the DNA tiles onto the solid surface, thus changing the tile assembly kinetics on the solid surface. Based on this discovery, we were able to promote or slow down DNA self-assembly on the surface by changing the hairpin locations on the DNA tiles. This knowledge gained will be helpful for the future design of DNA self-assembly on surface.

DNA Tile Self-Assembly Guided by Base Excision Repair Enzymes.

We demonstrate here the use of DNA repair enzymes to control the assembly of DNA-based structures. To do so, we employed uracil-DNA glycosylase (UDG) and formamidopyrimidine DNA glycosylase (Fpg), two enzymes involved in the base excision repair (BER) pathway. We designed two responsive nucleic acid modules containing mutated bases (deoxyuridine or 8-oxo-7,8-dihydroguanine recognized by UDG and Fpg, respectively) that, upon the enzyme repair activity, release a nucleic acid strand that induces the self-assembly of DNA tiles into tubular structures. The approach is programmable, specific and orthogonal and the two responsive modules can be used in the same solution without crosstalk. This allows to assemble structures formed by two different tiles in which the tile distribution can be accurately predicted as a function of the relative activity of each enzyme. Finally, we show that BER-enzyme inhibitors can also be used to control DNA-tile assembly in a specific and concentration-dependent manner.

Kinetics-Accelerated One-Step Detection of MicroRNA Through Spatially Localized Reactions Based on DNA Tile Self-Assembly

Kinetics-Accelerated One-Step Detection of MicroRNA Through Spatially Localized Reactions Based on DNA Tile Self-Assembly

Construction of nanostructures based on quadruplex DNA scaffolds

<p indent=0mm>DNA molecule served as the major carrier of genetic information has been proved to be an excellent assembly material in the construction of nanoscale structures. Over the past thirty years, various assembly methods of DNA nanomaterials have been established, including self-assembly of DNA tiles, DNA origami and other DNA nanotechnologies, based on specific complementary AT and GC base pairs. It is interesting to note that, in addition to traditional double helix structures, DNA molecules can also form other structures like triplex and quadruplex structures. Recently, people pay more attention to the study of quadruplex structures, including G-quadruplexes and I-motifs formed by G-rich and C-rich strands, respectively. It is because that quadruplex structures not only play significant roles in the regulatory regions of genes, but also can be programmed to construct DNA nanostructures due to their structural diversity and controllability during assembly. Here, this article mainly introduces the developments of DNA nanostructures assembled by quadruplex structures and describes their structural functionalities. First of all, the fabrications of DNA supramolecules formed by long telomeric sequences, short G-rich DNA strands and G-repeat-containing DNA strands are retrospected, which can assemble to be higher-ordered multimeric G-quad- ruplexes, G-wires, and G-quadruplex-linked DNA nanostructures, respectively. These assembled G-quadruplex nanostructures have potential to enhance the catalytic activity of G4/Hemin DNAzyme and act as a better candidate for conductive molecular nanowires. Subsequently, the DNA nanostructures assembled from long C-rich strands, short C-rich strands, C-repeat-containing strands and DNA sequences containing both G-repeat and C-repeat fragments are also discussed, which can form I-motif nanospheres, I-wires, I-motif-linked DNA nanostructures and quadruplex nanostructures, respectively. The pH-sensitivity of I-motifs can be used to construct DNA molecular machine, and map spatial and temporal pH changes in living systems, etc. From these results, we can conclude that the constructions of DNA nanostructures based on the self-assembly of DNA tiles or DNA origami have characteristics of mature technology and fine-structure mapping, which are also high cost and complexity of design; in comparison, these quadruplex-directed DNA nanostructures are relatively crude, which have advantages of low cost, structural controllability and simplicity in design. The combination of self-assembly of quadruplex scaffolds and DNA nanotechnology based on complementary base pairs may promote the wide applications of DNA nanomaterials in various areas.

Programming Self-Assembly of DNA Tiles

Programming Self-Assembly of DNA Tiles

In situ 2D-extraction of DNA wheels by 3D through-solution transport.

Controlled transfer of DNA nanowheels from a hydrophilic to a hydrophobic surface was achieved by complexation of the nanowheels with a cationic lipid (2C12N(+)). 2D surface-assisted extraction, '2D-extraction', enabled structure-persistent transfer of DNA wheels, which could not be achieved by simple drop-casting.

Parallel molecular computation of modular-multiplication with two same inputs over finite field GF(2n) using self-assembly of DNA tiles

Two major advantages of DNA computing – huge memory capacity and high parallelism – are being explored for large-scale parallel computing, mass data storage and cryptography. Tile assembly model is a highly distributed parallel model of DNA computing. Finite field GF(2n) is one of the most commonly used mathematic sets for constructing public-key cryptosystem. It is still an open question that how to implement the basic operations over finite field GF(2n) using DNA tiles. This paper proposes how the parallel tile assembly process could be used for computing the modular-square, modular-multiplication with two same inputs, over finite field GF(2n). This system could obtain the final result within less steps than another molecular computing system designed in our previous study, because square and reduction are executed simultaneously and the previous system computes reduction after calculating square. Rigorous theoretical proofs are described and specific computing instance is given after defining the basic tiles and the assembly rules. Time complexity of this system is 3n−1 and space complexity is 2n2.

Arithmetic Computation Using Self-Assembly of DNA Tiles: Subtraction in the Method of Complements

Arithmetic Computation Using Self-Assembly of DNA Tiles: Subtraction in the Method of Complements

Computation of Multiplicative Inversion and Division in GF(2&lt;SUP&gt;&lt;I&gt;n&lt;/I&gt;&lt;/SUP&gt;) by Self-Assembly of DNA Tiles

Computation of Multiplicative Inversion and Division in GF(2&lt;SUP&gt;&lt;I&gt;n&lt;/I&gt;&lt;/SUP&gt;) by Self-Assembly of DNA Tiles

Logical NAND and NOR Operations Using Algorithmic Self-assembly of DNA Molecules

Abstract DNA self-assembly is the most advanced and versatile system that has been experimentally demonstrated for programmable construction of patterned systems on the molecular scale. It has been demonstrated that the simple binary arithmetic and logical operations can be computed by the process of self assembly of DNA tiles. Here we report a one-dimensional algorithmic self-assembly of DNA triple-crossover molecules that can be used to execute five steps of a logical NAND and NOR operations on a string of binary bits. To achieve this, abstract tiles were translated into DNA tiles based on triple-crossover motifs. Serving as input for the computation, long single stranded DNA molecules were used to nucleate growth of tiles into algorithmic crystals. Our method shows that engineered DNA self-assembly can be treated as a bottom-up design techniques, and can be capable of designing DNA computer organization and architecture.

Solving River Crossing Puzzle in the DNA Tile Self-Assembly Model

Solving River Crossing Puzzle in the DNA Tile Self-Assembly Model

Design and experimental validation of a generic model for combinatorial assembly of DNA tiles into 1D-structures

BackgroundQuantitative modeling of the self-assembly of DNA tiles leading either to defined end-products or distribution of biopolymers is of practical importance for biotechnology and synthetic biology. MethodsThe combinatorial process describing tile assembly was implemented into a generic algorithm allowing quantitative description of the population of significant species accumulating during the reaction course. Experimental formation and characterization by optical and electrophoresis approaches of copolymers resulting from the self-assembly of a limited number of half-complementary tiles were used to define and validate generic rules allowing definition of model parameters. ResultsFactors controlling the structure and the dynamic of the oligomer population were evidenced for assemblies leading or not to defined end-products. Primary parameters were experimentally determined using rapid mixing experiments. Adjustment of simulations to experimental profiles allowed definition of generic rules for calculation of secondary parameters that take into account macro- and microenvironment of individual hybridization steps. In the case of copolymers, accurate simulation of experimental profiles was achieved for formation of linear assemblies. ConclusionsOverall length of species and structure of the DNA regions flanking the hybridization sites are critical parameters for which calculation rules were defined. The computational approach quantitatively predicted the parameters affecting time-course and distribution of accumulating products for different experimental designs. General significanceThe computational and parameter evaluation procedures designed for the assembly of DNA tiles into large 1D-structures are more generally applicable for the construction of non-DNA polymers by extremities-specific recognition of molecular blocks.

Implementation of the Timetable Problem Using Self-assembly of DNA Tiles

DNA self-assembly is a promising paradigm for nanotechnology. Recently, many researches demonstrate that computation by self-assembly of DNA tiles may be scalable. In this paper, we show how the tile self-assembly process can be used for implementing the timetable problem. First the timetable problem can be converted into the graph edge coloring problem with some constraints, then we give the tile self-assembly model by constructing three small systems including nondeterministic assigning system, copy system and detection system to perform the graph edge coloring problem, thus the algorithm is proposed which can be successfully solved the timetable problem with the computation time complexity ofΘ(mn), parallely and at very low cost.

Solving 0-1 Planning Problem Based on Self-Assembly of DNA Tiles

Solving 0-1 Planning Problem Based on Self-Assembly of DNA Tiles

Algorithm for Elliptic Curve Diffie-Hellman Key Exchange Based on DNA Tile Self-Assembly

Algorithm for Elliptic Curve Diffie-Hellman Key Exchange Based on DNA Tile Self-Assembly

Effective algorithm to encrypt information based on self-assembly of DNA tiles

We present an error-tolerance scheme to encrypt information in DNA structures based on a one-time-pad (OTP) cryptosystem that provides theoretically unbreakable security. The problem of the DNA-based OTP encryption is the loss of synchronization between the message and the encryption key due to the DNA property of accepting mismatched base pairs. We propose a new implementation idea of encrypting algorithm with the fourfold fault tolerance against mismatches than the ordinary DNA XOR operation. Although there are several problems to be solved toward the practical use at this moment, it is expected that the molecular computation using DNA tiles will enlarge the application possibility of the OTP cryptosystem.

Algorithm of Solving the Subset-Product Problem Based on DNA Tile Self-Assembly

Algorithm of Solving the Subset-Product Problem Based on DNA Tile Self-Assembly