Self-assembly Of DNA Molecules Research Articles

Self-assembly of DNA molecules at bio-interfaces and their emerging applications for biomedicines

Self-assembly of DNA molecules at bio-interfaces and their emerging applications for biomedicines

Self-Assembly of DNA molecules in magnetic Fields

In this work, a rich variety of self-assembled DNA patterns were obtained in the magnetic field. Herein, atomic force microscopy (AFM) was utilized to investigate the effects of the concentration of DNA solution, intensity and direction of magnetic field and modification of mica surface by different cations on the self-assembly of DNA molecules. It was found that owning to the change of the DNA concentration, even under the same magnetic field, the DNA self-assembly results were different. The in situ test results showed that the DNA self-assembly in an magnetic field was more likely to occur in liquid phase than in gas phase. In addition, whether in a horizontal or vertical magnetic field, a single stretched dsDNA was obtained in a certain DNA concentration and magnetic field intensity. Besides, the modification of cations on the mica surface significantly increased the force between the DNA molecules and mica surface, and further changed the self-assembly of DNA molecules under the action of magnetic field.

Self-Assembly of DNA Molecules: Towards DNA Nanorobots for Biomedical Applications.

DNA nanotechnology takes DNA molecule out of its biological context to build nanostructures that have entered the realm of robots and thus added a dimension to cyborg and bionic systems. Spurred by spring-like properties of DNA molecule, the assembled nanorobots can be tuned to enable restricted, mechanical motion by deliberate design. DNA nanorobots can be programmed with a combination of several unique features, such as tissue penetration, site-targeting, stimuli responsiveness, and cargo-loading, which makes them ideal candidates as biomedical robots for precision medicine. Even though DNA nanorobots are capable of detecting target molecule and determining cell fate via a variety of DNA-based interactions both in vitro and in vivo, major obstacles remain on the path to real-world applications of DNA nanorobots. Control over nanorobot's stability, cargo loading and release, analyte binding, and dynamic switching both independently and simultaneously represents the most eminent challenge that biomedical DNA nanorobots currently face. Meanwhile, scaling up DNA nanorobots with low-cost under CMC and GMP standards represents other pertinent challenges regarding the clinical translation. Nevertheless, DNA nanorobots will undoubtedly be a powerful toolbox to improve human health once those remained challenges are addressed by using a scalable and cost-efficient method.

DNA origami and the complexity of Eulerian circuits with turning costs

Building a structure using self-assembly of DNA molecules by origami folding requires finding a route for the scaffolding strand through the desired structure. When the target structure is a 1-complex (or the geometric realization of a graph), an optimal route corresponds to an Eulerian circuit through the graph with minimum turning cost. By showing that it leads to a solution to the 3-SAT problem, we prove that the general problem of finding an optimal route for a scaffolding strand for such structures is NP-hard. We then show that the problem may readily be transformed into a Traveling Salesman Problem (TSP), so that machinery that has been developed for the TSP may be applied to find optimal routes for the scaffolding strand in a DNA origami self-assembly process. We give results for a few special cases, showing for example that the problem remains intractable for graphs with maximum degree 8, but is polynomial time for 4-regular plane graphs if the circuit is restricted to following faces. We conclude with some implications of these results for related problems, such as biomolecular computing and mill routing problems.

Strength of DNA Sticky End Links

Sticky ends are unpaired nucleotides at the ends of DNA molecules that can associate to link DNA segments. Self-assembly of DNA molecules via sticky ends is currently used to grow DNA structures with desired architectures. The sticky end links are the weakest parts of such structures. In this work, the strength of sticky end links is studied by computational means. The number of basepairs in the sticky end and the sequence are varied, and the response to tension along the axis of the molecule is evaluated using a full atomistic model. It is observed that, generally, increasing the number of basepairs in the sticky end increases the strength, but the central factor controlling this parameter is the basepair sequence. The sticky ends are divided into two classes of low and high strength. The second class has strength comparable with that of a double stranded molecule with one nick in one of the strands. The strength of the first class is roughly half that of the strong sticky ends. For all strong sticky ends tested, the enhanced stability is associated with the formation of an unusually stable complex composed from two basepairs and two flanking bases of certain sequence. This complex rotates and aligns with the direction of the force allowing significant deformation and providing enhanced strength. This is similar to a mechanism recently suggested to enhance the mechanical stability of an RNA kissing loop from the Moloney murine leukemia virus. The model is tested against experimental structural data for sticky ends and against published simulation results for the stretch of double stranded DNA. The results provide guidance for the design of DNA self-assembled structures and indicate the types of sticky ends desirable if maximizing the strength and stability of these structures is targeted.

Synthesis and characterization of multi-helical DNA–silica fibers

Multi-helical DNA-silica fibers were synthesised by the self-assembly of DNA molecules with cationic organosilanes and silica sources. By electron microscopy images and circular dichroism spectra, three-level helical structures in the silica fibers have been revealed, i.e. the DNA double-helix, the secondary left-handed DNA packing and the tertiary right-handed twisting.

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.

Robust and Photocontrollable DNA Capsules Using Azobenzenes

Various three-dimensional structures have been created on a nanometer scale using the self-assembly of DNA molecules. However, ordinary DNA structures breakdown readily because of their flexibility. In addition, it is difficult to control them by inputs from environments. Here, we construct robust and photocontrollable DNA capsules using azobenzenes. This provides a method to construct DNA structures that can survive higher temperatures and can be controlled with ultraviolet irradiation.

Basic Logical Operations Using Algorithmic Self-Assembly of DNA Molecules

In recent years, DNA self-assembly is beginning to be seen as a practical vehicle for computation. A number of research groups have begun developing nanofabrication methods based on DNA self-assembly. Since the basic logical operations based on DNA molecules could be considered as the fundamental units of DNA computer architecture, how to achieve the basic logical operations based DNA self-assembly is explored in this paper. Original intention on tiling can be applied to the assembly and realization of circuits. These procedures can be realized on the molecular scale through the medium of self-assembled DNA tiles. One layer of self-assembled DNA tiles will be used as self-assembly the program or circuit that leads to the computation of a basic Boolean expression. For this purpose, a modified triple-crossover (TX) tiles which consist of two inputs and one output are used to execute molecular logical operations. The self-assembly of designed periodic one-dimensional arrays are composed of modified triple-crossover (TX) tiles, in which the intermolecular contacts are directed by sticky ends. Here, the paper makes a further to perform a one-dimensional algorithmic self-assembly of DNA triple-crossover molecules that can be used to execute five steps of a logical (cumulative AND and OR) operations on a string of binary bits.

DNA Origami as a Nanoscopic Ruler For Super-Resolution Microscopy

The possibility of highly parallel formation of nanostructures using self-assembly of DNA molecules provides a powerful tool for bottom-up fabrication. The DNA origami technique, involves folding a long single-stranded DNA scaffold using short DNA staple strands that can only bind at particular points along this scaffold. With this technique large numbers of identical structures can be assembled simultaneously in a single experiment. One of the most attractive features of the origami technique is the precise addressability of the DNA structures formed. Each staple strand can serve as an attachment point for many different kinds of molecules or other objects. Due to their small size, DNA nanostructures are commonly imaged using atomic force microscopy or electron microscopy, but with recent advances in far-field fluorescence microscopy beyond the diffraction limit (super-resolution microscopy), structures in the sub-200 nm regime become amenable also to optical analysis. We here show that the distance between fluorescently labeled staple strands bound on specific positions of rectangular DNA origami structures can be accurately determined using a variety of super-resolution techniques such as single-molecule high-resolution imaging with photo-bleaching (SHRImP), direct stochastic optical reconstruction microscopy (dSTORM), and Blink-Microscopy.

The encapsulation of DNA molecules within biomimetic lipid nanocapsules

Most of DNA synthetic complexes result from the self-assembly of DNA molecules with cationic lipids or polymers in an aqueous controlled medium. However, injection of such self-assembled complexes in medium like blood that differ from that of their formulation leads to strong instability. Therefore, DNA vectors that have physico-chemical properties and structural organisation that will not be sensitive to a completely different medium in terms of ionic and protein composition are actively sought. To this end, the goal here was to discover and optimize a nanostructured system where DNA molecules would be encapsulated in nanocapsules consisting in an oily core and a shell covered by PEG stretches obtained through a nanoemulsion process in the absence of organic solvent. This encapsulation form of DNA molecules would prevent interactions with external hostile biological fluid. The results show the entrapment of lipoplexes into lipid nanocapsules, leading to the formation of neutral 110 nm-DNA nanocapsules. They were weakly removed by the immune system, displaying an increased blood half-life, and improved carcinoma cell transfection, in comparison to the parent lipoplexes. Our results demonstrate that the fabrication of nanocapsules encapsulating hydrophilic DNA in an oily core that meet criteria for blood injection is possible.

Folding DNA to create nanoscale shapes and patterns

'Bottom-up fabrication', which exploits the intrinsic properties of atoms and molecules to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by 'top-down' methods. The self-assembly of DNA molecules provides an attractive route towards this goal. Here I describe a simple method for folding long, single-stranded DNA molecules into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide 'staple strands' to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting DNA structures are roughly 100 nm in diameter and approximate desired shapes such as squares, disks and five-pointed stars with a spatial resolution of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton molecular complex).

DNA-Directed Magnetic Network Formations with Ferromagnetic Nanoparticles

We formed a DNA network embedding ferromagnetic cobalt nanoparticles with a 12-nm diameter through a nanoscale self-assembly of DNA molecules on large-scale mica surfaces (12 mm x 12 mm); we then confirmed its structural characteristics with an atomic force microscope. Moreover, noncontact magnetic force microscope measurement revealed that some embedded cobalt nanoparticles have different directions of magnetization, similar to "bits" in magnetic data storage devices.