The fabrication of dna nanostructures begins with the self assembly of single stranded dna into small building block materials called tiles. By facile onestep self assembly, the crossshaped dnas cdnas assembled from phresponsive imotif sequences and targeted muc1 aptamerimmunoadjuvant cpgfused sequences cpgmuc1 were integrated into dna nanohydrogels with controllable size by the hybridization of dna linkers. Sep 26, 2003 a dna nanostructure consisting of four fourarm junctions oriented with a square aspect ratio was designed and constructed. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self. Genetic encoding of dna nanostructures and their self. We shall especially concentrate on dna nanotechnology, which has been demonstrated in recent years to be the most effective programmable selfassembly. Dna dependent macromolecular condensation drives self assembly of the meiotic dna break machinery.
Dna tiles bearing complementary sticky ends are then able to further self assemble into larger arrays with distinct topological and geometric features. Simulations document selfassembly of proteins and dna. Cytosine and dna self assembly righthanded crossovers of bform dna double helices are therefore unique in that they are. Periodic protein arrays were achieved by templated selfassembly of streptavidin. Dna nanotechnology is an area of current research that uses the bottomup, self assembly approach for nanotechnological goals. Here, dna nanoribbons, containing multiple specific binding sites, can serve as a template for ultrasmall copper nanocluster 0. Directing selfassembly of dna nanotubes using programmable seeds. The advent of dna origami technology greatly simplified the design and construction of nanometersized dna objects. Selfassembly is a process in which a disordered system of preexisting components forms an organized structure or pattern as a consequence of specific, local interactions among the components themselves, without external direction. Dna nanotechnology, specifically, is an example of bottomup molecular self assembly, in which molecular components spontaneously organize into stable structures. Using dna to program the self assembly of colloidal nanoparticles and microparticles w. Responsive self assembly is a general process in biological systems and is highly desired in engineered systems.
Algorithmic selfassembly of dna sierpinski triangles. The in vitro and in vivo results demonstrate that this platform selectively delivers anticancer drugs to target cells, releases them upon nir irradiation, and effectively inhibits tumor growth through thermochemotherapy. Dna biosensor by selfassembly of carbon nanotubes and dna. Pdf building blocks for dna selfassembly bilal shaw.
Nanotechnology is often defined as the study of materials and devices with features on a scale below 100 nanometers. Dna molecular structures and intermolecular interactions are. Sorensena, harold fellermanna, peter eggenberger hotzb, and martin m. Molecular selfassembly is the assembly of molecules without guidance or management from an outside source.
Logical computation using algorithmic selfassembly of dna. It remains difficult, however, to construct dna assemblies that are also. For lowering the cost of synthesizing dna strands and facilitating the assembly process, it is highly desirable to use a minimal number of unique strands for potential technological applications. Apr 22, 2014 the assembly of the tetrahedron represents the execution of a prescribed molecular program. Synergistic selfassembly of rna and dna molecules nature. Grafting dna oligonucleotides to colloidal particles leads to specific, reversible interactions between those particles.
Dnatemplated selfassembly of protein and nanoparticle. Recent work1,2,3 has demonstrated the self assembly of designed periodic twodimensional arrays composed of dna tiles, in which the intermolecular contacts are directed by sticky ends. We test this hierarchical self assembly concept with dna. Here we report an experiment using a linear array of dna triple crossover tiles to controllably template the self assembly of singlelayer or double. Depending on the sequence of the template, the resulting object may be a square.
This situation brings a great challenge to engineer. By integrating temporal with spatial control, here we demonstrate the developmental selfassembly of a dna tetrahedron, where a prescriptive molecular program orchestrates the kinetic pathways by which dna molecules isothermally self assemble into a welldefined threedimensional wireframe geometry. Dna lattice based on the selfassembly of multiple shorter synthetic. Hierarchical self assembly of dna into symmetric supramolecular polyhedra. Pdf hierarchical selfassembly of dna into symmetric. First, the self assembled monolayers of swnts on an amide platinum electrode were made by covalent linking of conh bonds. Their highresolution structures will help map new routes toward the rational design of selfassembling 3d dna crystals. Complete tripartite graphs leyda almod ovar, jane lee, meirose neal, heiko todt and jessica williams, stonehill college.
When the constitutive components are molecules, the process is termed molecular selfassembly. The dna self assembly technique has been rapidly developed especially since the dna origami was put forward. Periodic protein arrays were achieved by templated self assembly of streptavidin. Fisher school of physics, brandeis university, waltham, ma 02453. Since the early 1980s, it has been recognized that the information storage capacity of dna is ideal for programming the self assembly of nanostructures 1. Pdf molecular selfassembly strategies involve the formation of nanometer scale objects and materials in the absence of significant external. Dna is thus used as a structural material rather than as a. However, the interaction strength varies steeply and monotonically with temperature, hindering the use of dna mediated interactions in self assembly. Design and selfassembly of twodimensional dna crystals nature.
Conceptually, algorithmic self assembly naturally spans the range between maximal simplicity the periodic order of. The use of dna for nanotechnology has gained interest because it is a highly programmable polymer with sticky ends, allowing the self assembly of molecular scaffolds for other proteins and molecules. Formation of meiotic dna doublestrand breaks dsbs by spo11 is tightly regulated and tied to chromosome structure, but the higherorder assemblies that execute and control dna breakage are poorly understood. Then, dna was attached to swnts film via carboxylamine coupling. However, each trigger requires a unique mechanism for its response. Colloidal interactions and self assembly using dna hybridization paul l. A dna nanostructure consisting of four fourarm junctions oriented with a square aspect ratio was designed and constructed. The use of dna for nanotechnology has gained interest because it is a highly programmable polymer with sticky ends, allowing the selfassembly of molecular scaffolds for other proteins and molecules.
Dna has recently been used as a programmable smart building block for the assembly of a wide range of nanostructures. N a technique in which small dna strands staples guide the selfassembly of a longer strand. Self assembling dna tiling lattices represent a versatile system for nanoscale construction. A realisation of the potential of dna origami, and of dna selfassembly in general, to create functional nanoscale devices has. Focus on dna nanostructures and selfassembly new journal of. View the article pdf and any associated supplements and figures for a period of 48 hours. Pdf algorithmic selfassembly of dna semantic scholar. Hybrid nanostructures from the selfassembly of proteins and dna. Mar 24, 2017 figure3 schematic illustration of the self assembly of dna protein hybrid objects from a set of 12 doubletal staple proteins and a template dna double strand.
This talk will focus particularly on molecular self assembly, giving examples of engineered dna tiles that crystallize into twodimensional sheets, onedimensional tubes and ribbons, and informationguided patterns such as a sierpinski triangle and a binary counter. However, those experiments in no way required a high concentration of assemblies and no. Mohammed and rebecca schulman, chemical and biomolecular engineering and computer science, johns hopkins university, baltimore, maryland 21218, united. Dnatemplated selfassembly of protein arrays and highly. The assembly of the tetrahedron represents the execution of a prescribed molecular program. Different nucleotide sequences yield complementary strands that direct short singlestranded dna ssdna to hybridize with high specificity into a set of branched junctions, including the crossover 2 and. Dna star motifs are a family of dna nanostructures with 3, 4. Using three dimensional graph structure and dna self assembly we show that theoretically 3sat and 3colorability can be solved in a constant number of laboratory steps. Selfassembly is the process in which a systems componentsbe it molecules, polymers, colloids, or macroscopic particlesorganize into ordered andor functional structures or patterns as a consequence of specific, local interactions among the components themselves, without external direction. Selfassembly of hydrogels with uniform surface dna glues. Mar 28, 2018 in nature, these phenomena often occur in particles that are suspended in a mediumreferred to as colloidal particlessuch as proteins, dna and rna.
Selfassembly of large dna origami with customdesigned. Supporting information as a service to our authors and readers, this journal provides supporting information supplied by the authors. Threedimensional structures selfassembled from dna. As a milestone in dna self assembly, dna origami has demonstrated powerful applications in many fields.
Their highresolution structures will help map new routes toward the rational design of self assembling 3d dna crystals. Developmental selfassembly of a dna tetrahedron acs nano. Selfassembly dna polyplex vaccine inside dissolving. Thus encouraged, i have begun an experimental investigation of algorithmic self assembly. Colloidal interactions and selfassembly using dna hybridization. The study of selfassembly of nanoparticles began with recognition that some properties of atoms and molecules enable them to arrange themselves into patterns. In this work, dna self assembly is a onepot process. Conformational flexibility facilitates selfassembly of. Here we report the noncanonical selfassembly of multifunctional dna nanostructures, termed as nanoflowers nfs, and the versatile biomedical applications. Self assembly of nucleic acids dna and rna provides a powerful approach for constructing sophisticated synthetic molecular structures and devices 1. Transient or longterm dna self assembly participates in essential genetic functions. Selfassembly of genetically encoded dnaprotein hybrid. Conceptually, algorithmic selfassembly naturally spans the range between maximal simplicity the periodic order of.
This onestep synthesis of self assembly dna polyplex vaccine inside mns is simpler than those reports that must prepare polyplex first then loaded in mns 22, 28, 29. Paulson school of engineering and applied sciences, harvard university, cambridge, ma 028 2martin a. The assembly of nanoparticles into threedimensional 3d architectures could allow for greater control of the interactions between these particles or with molecules. Dnadependent macromolecular condensation drives self. The assembly of swnts and dna via chemical approach on an aminemodified platinum electrode surface was proposed in this paper. This paper describes our recent efforts on the self assembly of threedimensional 3d dna nanostructures from dna star motifs tiles. Kinetically controlled selfassembly of dna oligomers. Molecular selfassembly presents a bottomup approach to the fabrication of objects specified with nanometre precision. A variety of applications where the selfassembly of nanoparticles might be useful. Molecular self assembly presents a bottomup approach to the fabrication of objects specified with nanometre precision.
A competition experiment suggests that an individual logical step can proceed correctly by self assembly, while a companion experiment demonstrates that unpatterned two dimensional lattices of dna will self assemble and can be visualized. We examine self assembling dna from a graph theory perspective based on the tile model. In this study, we present a robust strategy to produce long circular ssdna scaffold strands with. We will overview theoretical principles and techniques such as tiling assemblies and molecular transducers developed for a number of dna selfassembly. N a technique in which small dna strands staples guide the self assembly of a longer strand. In this assembly, junction molecules and duplex dna molecules are the basic. In this study, we present a robust strategy to produce long circular ssdna scaffold strands with customtailored. Self assembly can occur spontaneously in nature, for example, in cells such as the self assembly of the lipid bilayer membrane. These squares were assembled into 8 8 a rrays that had customized surface patterns. Atptriggered, allosteric selfassembly of dna nanostructures. Dna nanostructures provide a versatile molecular platform for studying such responsive self assembly. Dnadirected selfassembly of shapecontrolled hydrogels. Pdf nanofabrication by dna selfassembly researchgate.
Dna mediated assembly of plasmonic heteropentamers. Crocker2 1department of physics and astronomy, university of pennsylvania, philadelphia, pennsylvania 19104, usa. One nanometer selfassembled aptamerdna dendrimers carry. We address this question through molecular characterization of saccharomyces cerevisiae rmm proteins rec114, mei4 and mer2essential, conserved components of the dsb machinery. Self assembly is the process in which a systems componentsbe it molecules, polymers, colloids, or macroscopic particlesorganize into ordered andor functional structures or patterns as a consequence of specific, local interactions among the components themselves, without external direction. Algorithmic selfassembly of dna thesis by erik winfree in partial ful. Design and selfassembly of twodimensional dna crystals. By the attachment of singlestranded dna to gold nanoparticles. Pdf dnatemplated selfassembly of protein arrays and. Structures have been designed by encoding sequence complementarity in dna strands in such a manner that by pairing up complementary segments, the strands self organize into a prescribed target. Self assembled dna arrays provide an excellent template for spatially positioning other molecules with increased relative precision and programmability. Periodic protein arrays were achieved by templated self assembly.
Figure 1 methods for making micrometrescale dna objects. To achieve active self assembly, a synergy of diverse dna techniques is essential, including structural design, controllable assembly disassembly, autonomous assembly, molecular circuits, biochemical oscillators, and so on. Dna nanotechnology uses the unique molecular recognition properties of dna and other nucleic acids to create self assembling branched dna complexes with useful properties. Mediated by watsoncrick basepairing, these dna nanostructures have been conventionally assembled through hybridization of many short dna building blocks. Experiments in dna self assembly commonly contain on the order of 10 17. Such control is crucial since future nanoelectronic devices assembled on a dna based molecular printboard would require the dna scaffolds to have defined boundaries. Using dna to program the selfassembly of colloidal.
Our initial attempt to assemble such hydrogel cubes carrying short. Towards active selfassembly through dna nanotechnology. Depending on the sequence of the template, the resulting object may be a square top or a doublering circle bottom. Figure3 schematic illustration of the self assembly of dna protein hybrid objects from a set of 12 doubletal staple proteins and a template dna double strand. It usually results in an increase in internal organization of the system. Among them, dna self assembly has drawn much attention because of their precise and rigorous base pairing, predictable spatial structures, fixed pitch and doublestrand height together with simple synthesis and flexible sequence design.
Various triggers have been explored for dna nanostructures. Directing selfassembly of dna nanotubes using programmable seeds abdul m. Dna tubes are known to form through either self association of multihelix dna bundle structures or closing up of 2d dna tile lattices. Corentin claeys bouuaert1,2, stephen pu1, juncheng wang3, dinshaw j. Rna strands are guided by dna strands to selfassemble into hybrid rnadna branched motifs. The program is depicted as a reaction graph using a nodal abstraction that concisely describes the kinetic pathways by which dna reactants self assemble and disassemble. Often many dna strands are required for the assembly of one dna nanostructure. However, the scarce availability of long singlestranded dna ssdna limits the size and sequences of dna origami nanostructures, which in turn impedes the further development. Selfassembly of symmetric finitesize dna nanoarrays. Nov 19, 2012 in summary, we have developed a targeted nirresponsive np delivery platform by a simple dna self assembly process. The emergence of structural dna nanotechnology has enabled us to design the self. Pdf computation by selfassembly of dna graphs phiset.
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