Top PDF Algorithmic self-assembly of DNA

Algorithmic self-assembly of DNA

Algorithmic self-assembly of DNA

A definitive answer to “But will it work?” requires a chemist’s knowledge and actual experi- ments. But we can immediately bring some more concerns to light. Since I do not have answers to them, I will merely mention them in passing. First, to read out an answer of more than one bit, our implementation requires ligating the rule molecules and cutting them with resolvase. It is not at all clear that, in the crowded confines of the DNA lattice, either ligase or resolvase will have room enough to perform its job 14 . Second, it is possible that, at a low rate, incorrect rules will be incorporated into the lattice. If this occurs, the computation is ruined. It is thus not clear at this time what yields of correct computation are to be expected, and whether a means could be devised to separate the good from the bad. It is additionally conceivable that stable structures form in the solution unconnected to the initial molecule. For example, four rules molecules could connect in a stable “diamond”; we might think that these complexes will only rarely be formed, because the intermediate steps are unstable (only one sticky end joins molecules), and for similar reasons they would grow slowly. However, they and other types of spurious connections and tangles could form, ruining the computation. A final concern is that there may be some systematic molecular stress or strain that comes into play when building a large crystal, and that beyond a certain size tearing would result. All these issues, and surely others, deserve more attention and study.
Show more

109 Read more

Crystals that Count! Physical Principles and Experimental Investigations of DNA Tile Self Assembly

Crystals that Count! Physical Principles and Experimental Investigations of DNA Tile Self Assembly

Our results are preliminary, and need to be expanded. However, they do show that accurate algorithmic self-assembly is possible at present with improved technologies. The counters seen with our newer strands were by no means elusive; they were the product of our first attempt at growth with the reordered strands, and did not require precise optimization of concentrations or temperatures. We hope that further results may be able to improve upon what we have already seen, and also result in finite, programmable structures through capping. The types of errors that we see warrant some further analysis. Despite several counting errors being possible from the lack of full proofreading and seen in simulations, only one type has been seen experimentally. This may suggest that facet nucleation is a larger problem than might be expected. Width-change errors, seen both in our results and earlier ribbon experiments [4, 64], seem to occur through lattice defects that aren’t considered in the kTAM. Furthermore, overflow behavior may be different experimentally and in the kTAM, with simulations often changing width at overflows. All of these factors may indicate areas where experiments may diverge from the kTAM. Analyzing the relative prevalence of different errors and the ways they arise in simulation and more extensive experimental results could prove insightful.
Show more

91 Read more

DNA Self-assembly Model for Matrix Addition Problem

DNA Self-assembly Model for Matrix Addition Problem

DNA tile self-assembly is looked forward to many applications in different fields. More and more scientists have paid their attention on this field. Therefore, DNA computation based on self-assembly has been playing a significant role in bio-molecular computing. Mao [8] came up with triplecrossover to execute four steps of logical (cumulative XOR) operations on a string of binary bits. These kinds of tiles are more stable and rigid which ensure that the process of tile assembly can achieve our desired computation. Barish et al.[9] have proposed an algorithmic self-assembly to perform two primitive computations: copying and counting, and experimentally demonstrated the potential of algorithmic self-assembly to create complex nano-scale patterns. Fujibayashi et al. [10] have used DNA tiles and DNA origami to grow crystals containing a cellular automaton pattern and proved that programmable molecular self-assembly may be sufficient to create a wide range of complex objects in one-pot reactions. Dwyer and his research group [11] have proposed two architectures that are enabled by self- assembly for implementation of DNA computers solving highly demanding computational problems.
Show more

7 Read more

PH-Controlled Assembly of DNA Tiles

PH-Controlled Assembly of DNA Tiles

The pH controllable catalyst can be used to direct the assembly of DNA nanostructures using pH. To do this we have interconnected the above-characterized pH-dependent circuit with a DNA tile self-assembly process. 10,11a,11b,12 Fluorescence microscopy images (Fig. 3, top) and AFM images (Fig. 3, center) confirm that tiles assemble only at neutral/basic pHs, while no assemblies are observed over the same reaction time at acidic pHs (pH 5.0 and 6.0). Tile assembly largely yields tubular structures according to fluorescence microscopy and AFM images. As a control experiment we used a pH- independent substrate and observed assembly of DNA tiles in the entire pH range investigated (Fig. 3, bottom). Moreover, statistical analysis shows that the length and yield of nanotubes formed with the pH-dependent substrate under basic conditions (average length = 0.91 m and yield = 23 10%, at pH 8.0) is comparable to those of the control pH- independent substrate at both pH 8.0 (length = 0.75 m and yield = 12 6%) and 5.0 (length = 0.79 m and yield = 19 12%) (for details see experimental section and Fig. SI8). As a further demonstration that pH does not affect the downstream tile assembly reaction, we have exogenously added the Deprotector to a solution containing protected tiles and observed pH-independent tile assembly (Fig. SI9). Conversely, the absence of Catalyst leads to no nanotubes formation (Fig. SI10).
Show more

12 Read more

Diverse Colloidal Crystals And Clusters Formed By Dna-Grafted Spheres Via Self-Assembly

Diverse Colloidal Crystals And Clusters Formed By Dna-Grafted Spheres Via Self-Assembly

crystal lattice, contain multiple negative curvature spherical ‘dimples’ arranged either with tetrahedral or cubic symmetry, depending on whether they were compressed in the host lattice’s tetrahedral or octahedral sites. Analysis of the particle shape indicates that they resemble three-dimensional capillary bridges, which can deform the host lattice to minimize the droplet’s capillary energy. The yield of different symmetries depends on the size ratio of the droplets to the host-lattice particles; up to 25% (for tetrahedra) and 35% (for cubes) of solid TPM particles have the desired regular symmetry, with the remainder being primarily undimpled spheres. Centrifuging the resulting mixtures of particles in a density gradient allows their dispersion according to their sedimentation velocity, and thus symmetry. Significant enrichment of some particle symmetries was demonstrated with this technique, with the major impurity being below-nominal sized spheres. Even at the small scale of current experiments, ~10 8 micron-sized tetrahedral particles can be obtained in a single batch. As a three-dimensional technique, we anticipate that the mass of particles produced per batch is readily scalable, opening the door to future self-assembly experiments. The physics of colloidal crystal templating and droplet wetting also scales, and so these methods should allow the size of the resulting dimpled particles (roughly 1 µm here) to be scaled down if desired.
Show more

146 Read more

Self-Assembly DNA Polyplex Vaccine inside Dissolving Microneedles for High-Potency Intradermal Vaccination

Self-Assembly DNA Polyplex Vaccine inside Dissolving Microneedles for High-Potency Intradermal Vaccination

Skin vaccination is an alternate route of immunization that increases vaccine immunogenicity [12]. The skin’s layers are known to have abundant professional antigen-presenting cells (APCs; i.e., macrophages, Langerhans cells, and dendritic cells), which play an important role in inducing immune responses [13, 14]. Currently, injection with a hypodermic needle is the most commonly used method of administering vaccines, but this technique is painful, has low patient acceptance, and cannot deliver the vaccines to the epidermis. Recently, an alternative vaccination method has been developed: an easy-to-apply microneedle (MN) patch, which addresses these concerns by offering a more patient-compliant and safer method of administering vaccines into the epidermis and superficial dermis by minimally trained personnel [15, 16], enabling increased vaccine thermostability and generating no sharps waste [17-19]. In previous studies, MNs coated with naked DNA vaccines have been used to significantly increase the antibody- and cell-mediated immune responses. However, the repeated dip-coating and drying of highly concentrated and viscous DNA vaccine solutions necessary for MN manufacture cause initial activity loss [20, 21]. Another approach is the layer-by-layer deposition of polyelectrolytes and DNA vaccines on the surface of MNs, which precisely controls the DNA loading amount and avoids initial activity loss [22-24]. However, the coated DNA vaccines can be scraped away from the MN surface by skin tissues (especially the stratum corneum) during insertion, reducing the amount of vaccine in the epidermis. To overcome this problem, dissolving MNs were designed to protect the vaccines by their entrapment inside the MN using casting procedures (vacuum or centrifugation). These MNs only dissolve in the interstitial fluid of the skin
Show more

13 Read more

Self-Replication and Self-Assembly for Manufacturing

Self-Replication and Self-Assembly for Manufacturing

If we can create a mechanism for controlling the size and shape of the mesh, more applications become possible. Since the system is accurate and self-correcting, pieces of cloth could be created exactly to specification, down to the size of a single machine. The design of the individual machines in JohnnyVon is too complex to be implemented at the nanoscale, given the current state of the art of nanotechnology. However, the machines appear to be less complex than typical virsuses, which range in size from about 20 to 250 nanometers. Nanoscale is generally defined as about 1 to 100 nanometers. As mentioned earlier, JohnnyVon 2.0 was partly inspired by Seeman’s work with DNA [14], [15]. A single DNA molecule is about 2 nanometers wide. JohnnyVon’s design is somewhat different from Seeman’s work, so it would not be accurate to describe his work as an implementation of JohnnyVon, but it does seem reasonable to say that JohnnyVon could be implemented at the nanoscale, given improvements in the state of the art.
Show more

45 Read more

Design, Synthesis, and Characterization of Nanoscale Optical Devices Using DNA Directed Self-Assembly

Design, Synthesis, and Characterization of Nanoscale Optical Devices Using DNA Directed Self-Assembly

Negatively stained transmission electron microscope (TEM) images of successfully synthesized structures are shown to the right of each design schematic in Figure 2.1. As can be seen from the images, each target design was successfully synthesized, confirming the power of DNA-directed self-assembly in controlling both nanoparticle spacing and spatial arrangement. The TEM sample preparation is described in Section 2.6.2. Despite a high nanoparticle attachment yield, generally above 90 percent, characterization of the 1xD1, 1xD2 and 1xT waveguides revealed that AuNPs could fall on either side of the nanotube when depositing them on a substrate. This deviation from linearity was sufficient to cause the polarization dependence of the waveguides’ scattering spectra to be poorly defined, as discussed below. Several examples are shown in Section 2.6.3. To better control the orientation and location of the AuNPs and to increase the mechanical rigidity of the waveguides, plasmonic waveguide arrays assembled on two DNA origami nanotubes were developed.
Show more

227 Read more

Directed Self Assembly: Expectations and Achievements

Directed Self Assembly: Expectations and Achievements

mind that lithography itself can conveniently be used to direct the growth. Unsatisfied bonds have been conve- niently used as chemical templates. Similarly, biologists too have employed bio-alignments (DNA as template is one example). Electric field, excimer laser, light, magnetic field, pressure gradient, shear gradient and various fields have been employed to achieve functional nanostructures by field-directed self-assembly. Here in this review, use of electric field and laser has been described in detail. How- ever, magnetic field [89, 90] and focused ion beam [91] are the other two fields as competitive for the purpose of directed self-assembly of materials. Directed self-assembly of nanomaterials as a discipline is quite versatile in nature. Guise et al. [92] has achieved patterning of sub-10-nm Ge islands on Si(100) by directed self-assembly. Greve et al. [93] have dealt with the directed self-assembly of amphi- philic regioregular polythiophenes on the nanometer scale. Xu et al. [94] have demonstrated directed self-assembly of block copolymers on two-dimensional chemical patterns fabricated by electro-oxidation nanolithography. Gupta et al. [95] have described the entropy-driven segregation of nanoparticles to cracks in multilayered composite polymer structures. Adam et al. [96] have used NHO hydrogen bonding for directed self-assembly and achieved a trilay- ered supramolecular array formed between 1,2-diaminoe- thane and benzoic acid. Lee et al. [97] have achieved self-assembly of 2,6-dimethylpyridine on Cu(1 1 0) direc- ted by weak hydrogen bonding. Kinge et al. [98] have reviewed self-assembling of nanoparticles at surfaces and interfaces. Sitti [99] has demonstrated high aspect ratio polymer micro/nanostructure manufacturing using directed self-assembly.
Show more

10 Read more

A supramolecular assembly mediates lentiviral DNA integration

A supramolecular assembly mediates lentiviral DNA integration

Abstract: Retroviral integrase (IN) functions within the intasome nucleoprotein complex to catalyze the insertion of viral DNA into cellular chromatin. The lack of lentiviral intasome structural information has hampered the development of anti-HIV drugs and the understanding of viral resistance. Using cryo-electron microscopy, we now visualize the functional maedi-visna lentivirus intasome at 4.9 • resolution. The intasome, which comprises a homo-hexadecamer of IN with a tetramer-of-tetramers architecture, harbors eight structurally distinct types of IN protomers including two catalytically competent subunits. The conserved intasomal core, previously observed in simpler retroviral systems, is formed between two IN tetramers, with a pair of C- terminal domains from flanking tetramers completing the synaptic interface. Our results explain how HIV-1 IN, which self-associates into higher order multimers, can form a functional intasome, reconcile the bulk of early HIV-1 IN biochemical and structural data, and provide a lentiviral platform for structure-guided design of HIV-1 IN inhibitors.
Show more

14 Read more

Enhancement of RecA-mediated self-assembly in DNA nanostructures through basepair mismatches and single-strand nicks

Enhancement of RecA-mediated self-assembly in DNA nanostructures through basepair mismatches and single-strand nicks

A nick in the phosphate backbone of one of the strands of the dsDNA adjacent to the assembly site leads to increased breathing in the vicinity of the nick and therefore is expected to lead to increased assembly yields of the RecA-based nucleoprotein filaments. Figure 6 shows the assembly yields for both types of scaffolds discussed above, together with the yield for a scaffold featuring a nick directly adjacent to the assembly site. Indeed, the assembly yield increases to over 85% upon introduction of the nick, providing further confirmation that these topologies are able to provide significant increases in patterning efficiency. Although significant, the increase in yield associated with a nick in the backbone is not as high as with regions of base pair mismatches proximal to the patterning site. It is likely that the hydrophobic effect and π - π interactions between the bases of the strand prevent the same level of breathing as would be observed at the terminus of a strand, and thus nicking only leads to smaller increases in patterning efficiency. The results of RecA-based nucleoprotein assembly onto scaffolds in which the position of the nick is varied is reported in Supplementary Figure S5a.
Show more

9 Read more

The Power of Nondeterminism in Self-Assembly

The Power of Nondeterminism in Self-Assembly

A practical implementation of self-assembling molecular tiles was proved experimentally feasible in 1982 by Seeman [42] using DNA complexes formed from artificially synthesized strands. Experimental advances have delivered increasingly reliable assembly of algorithmic DNA tiles with error rates of 10% per tile in 2004 [38], 1.4% in 2007 [20], 0.13% in 2009 [7], and 0.05% in 2010 [17]. Erik Winfree [49] introduced the abstract Tile Assembly Model (aTAM)—based on a constructive version of Wang tiling [47, 48]—as a simplified mathematical model of self-assembling DNA tiles. Winfree demonstrated the computational universality of the aTAM by showing how to simulate an arbitrary cellular automaton with a tile assembly system. Building on these connections to computability, Rothemund and Winfree [39] investigated a self-assembly resource bound known as tile complexity, the minimum number of tile types needed to self-assemble a shape. They showed that for most n, the problem of self-assembling an n × n square has tile complexity Ω(log(n)/ log log(n)), and Adleman, Cheng, Goel, and Huang [3] exhibited a construction showing that this lower bound is asymptotically tight. We discuss two different models of self-assembly below (unique versus strict), but both of the previous results hold for either model. Under natural generalizations of the model [1, 5, 8, 10–14, 19, 22, 23, 32, 44, 46], tile complexity can be reduced for tasks such as square-building and self-assembly of more general shapes. We now briefly describe the aTAM; a formal definition is given in Section 2. A tile in the aTAM is a unit square with a kind and strength of “glue” on each of its sides. Tiles are assumed not to rotate so that each side has a well-defined direction: north, south, east, or west. A tile assembly system T = (T,σ ,τ) consists of a finite set T of tile types (with infinitely many tiles of each type in T available), a seed tile σ ∈ T , from which growth is assumed to nucleate, and a temperature τ , assumed to be 2 in this paper. Self-assembly proceeds from the seed tile σ , with tiles of types in T successively attaching themselves to the existing assembly. Two tiles placed next to each other interact if the glues on their abutting sides match, and a tile binds to a binding site on an assembly if the total strength on all of its interacting sides is at least τ . The choice of which binding site to attach is nondeterministic. It is possible that a single binding site could have more than one tile type able to attach with strength τ, which is also a choice made nondeterministically (the impossibility of this situation occurring precisely characterizes the “directed” tile systems, described informally next and defined formally in Section 2).
Show more

29 Read more

Multifunctional Nanomaterials of DNA Block Copolymers: Synthesis, Self- Assembly, Thermodynamic Studies and Biomedical Applications

Multifunctional Nanomaterials of DNA Block Copolymers: Synthesis, Self- Assembly, Thermodynamic Studies and Biomedical Applications

The PL spectrum of the Cy3-DNA and simple micelle mixture in water (Figure 3- 5 C) shows a strong FAM peak at 520 nm, indicating that the complementary Cy3-DNA does not bind to the small micelles of PS@DNA in water without added salts. On the other hand, the meso-assemblies showed an intense Cy3 peak at 564 nm and a reduction of FAM peak intensity at 520 nm, indicating that Cy3-DNA strands hybridize to the complementary DNA on meso-assemblies at an extremely low salt concentration (Figure 3-5D). This behavior is similar to what was found for the assemblies encapsulated with magnetic nanoparticles (MNP@PS@DNA) in our previous report. 2 The FRET efficiency between the meso-assemblies incorporating PS homopolymers and Cy3-DNA in water was calculated to be 74.6 ± 4.1%. This result clearly shows that the enhanced DNA binding property of our meso-assemblies is indeed size-dependent phenomena. It also shows that the enhanced binding is not nanoparticle-specific, such that any core-filled meso-assemblies of DNA block copolymers possess enhanced DNA binding properties regardless of the type of core-filling materials. Thus, one can combine the unusual enhanced binding properties of meso-assemblies with any types of molecular or nanoscale encapsulants.
Show more

227 Read more

Beyond Watson and Crick: Programming the Self-Assembly and Reconfiguration of DNA Nanostructures Based on Stacking Interactions

Beyond Watson and Crick: Programming the Self-Assembly and Reconfiguration of DNA Nanostructures Based on Stacking Interactions

Figure 1. Design and modelling of DNA nanotubes. (A) Top: a single tile REs, based on the core RE, bears 4 sticky ends. Bottom: Complementarity between sticky ends directs the tiles to form a regular lattice. (B) A single tile SEs, based on a difference core SE, and its lattice. (C) Two tiles, REd and SEd, can assemble into a lattice with diagonal stripes; alone each tile could assemble into a linear strip. (D) Another pair of tiles, REp and SEp, cannot assemble independently but together can form a lattice with stripes perpendicular to the long axis of the tiles. (E) Structure of a DAE-E molecule. Each tile is assembled from five single strands: two of 37 nucleotides (nt) (top and bottom, no. 1 and no. 5, red and magenta), two of 26 nt (left and right, no. 2 and no. 4, yellow and green) and one of 42 nt (central, no. 3, blue). Triangles mark two crossover points, separated by two helical turns (21 nt). Arrowheads point from 5" to 3". Sticky ends (5 nt) are at the ends of the no. 2 and no. 4 strands. (F) Tile structure with hairpins (8 nt stem, 4 nt loop) on the no. 1 and no. 5 strands between the 14th and 15th nt from their 5" ends. Molecular models suggest that these hairpins attach underneath the molecule, as depicted here; in a tube they would be on the outside. (G and H) Two in-plane rotational symmetries that, if satisfied by a patch of tiles, encourage molecular strain to balance, resulting in a flat sheet. (I) A rotational symmetry, satisfied by DAE-E molecules, that permits curvature. (J) Heptagonal tube of radius R. In each tile, two cylinders of radius r represent the double-helices. Black circles mark crossover points. Blue and orange lines connect the position of phosphate backbones to the center of a helix. The smaller angle between the blue and orange lines defines the minor groove. Tiles from (A), (B), or (D) may form tubes of any number of tiles in circumference; tiles from (C) only tubes of an even number. (K) Cross-section of the red tile from (J) at a crossover point.
Show more

144 Read more

Engineering a Library of Anisotropic Building Blocks for DNA-Programmed Colloidal Self-Assembly

Engineering a Library of Anisotropic Building Blocks for DNA-Programmed Colloidal Self-Assembly

A simple and effective method of circumventing the segregation issue is to com- pletely eliminate all DNA interactions during crystallization, and to drive crystal formation by other means, such as sedimentation. In this experiment, a mixture of P and P 0 particles, with the ratio used above, is first prepared in a buffer with no added salt, which effectively turns off all attractive DNA interactions at room temperature. Due to the small size of our particles, sedimentation is performed in a low-speed benchtop centrifuge overnight, forming a dense pellet of particles. The salt concentration in the supernatant is then increased from 0mM to 150mM NaCl in multiple addition steps consisting of gentle pipette mixing and further centrifuga- tion, turning on all attractive interactions and stabilizing the assembled structure at room temperature. The resultant pellet has large crystalline domains having a close packed structure, which can be broken apart manually and visualized by microscopy, Figure 3.4c,d. As expected, the impurity particles are well dispersed.
Show more

144 Read more

DNA as a vehicle for the self assembly model of computing

DNA as a vehicle for the self assembly model of computing

Self-assembly computing utilizes parallelism in a very different way than Adleman type schemes. The new feature is that the search space is ex- plored by the different pathways of conforma- tional self-organization subsequent to duplex formation, whereas in the Adleman scheme they are explored by the number of hybridization path- ways. The latter in general generates an exponen- tially increasing number of reaction products. The number of sequences is initially small but in- creases as the reaction proceeds. This is because the search is implemented by a branching reac- tion. In this way fine grained parallelism is used to exhaustively search the space of potential solu- tions. By contrast, the number of DNA molecules decreases as the computation performed by the self-assembly processor proceeds. This is because all the input sequences aggregate with the back- bone to yield a single species of double stranded DNA. The important distinction between the two models is this: the Adleman scheme draws its computational power from the sequence matching aspect of hybridization, whereas the self-assembly scheme draws its power from the conformational dynamics concomitant to this sequence matching. We can finally consider how the amount of DNA required by the self-assembly processor scales with problem size. For a given pattern classification problem the search space increases as 2 n , where n is the number of signal lines. This
Show more

8 Read more

Computational Study of DNA-Directed Self-Assembly of Colloids

Computational Study of DNA-Directed Self-Assembly of Colloids

The phase diagram for a hard-sphere system can be expanded by introducing an additional degree-of-freedom, such as colloidal size polydispersity (Fig. 4.2). The system’s free energy arises purely from entropy – the assembly of the maximum close- packed superlattice [20, 44]. With the addition of a very-short ranged attractive interaction, the colloidal superlattice structure will not vary appreciably (only a slight decrease of its volume fraction); now each colloid centered at its superlattice site will oscillate around the minimum of the interaction potential. It is vital that the potential allows for annealing of the colloids, i.e. the potential well-depth must be shallow enough to allow colloids to enter and leave via thermal fluctuations; without this mechanism crystallization into any superlattice structure is impossible.
Show more

174 Read more

Engineering Molecular Self-assembly and Reconfiguration in DNA Nanostructures

Engineering Molecular Self-assembly and Reconfiguration in DNA Nanostructures

Since the creation of the first DNA origami, there has been interest in scaling up the size of two dimensional DNA origami structures (see Fig 4.0). Marchi et al. [1] took the direct approach to increasing the scale of a DNA origami structure by taking the same principles as the first DNA origami but applied to a significantly longer scaffold strand. With a single scaffold strand for the staples to attach onto, the author's overall DNA structure maintains the benefit that it can still be made in a single mixing step. However, as the number of unique locations to be held together increases due to a longer scaffold, so does the number of unique staple strands needed to form the complete DNA structure. More unique strands means a higher upfront cost and issues with spurious interactions among the distinct strands. Raiendran et al [2] implemented a scaled DNA structure requiring fewer additional unique staples through the use of select recycled staples. The authors split the mixing stages into two steps: in the first, nine individual DNA origami tiles were annealed reusing many staple sequences between the separate tile's interiors; in the second, the nine DNA origami tiles were mixed together, and due to their unique edges, formed a 3 by 3 array. Accordingly, a DNA structure nine times the size of a single DNA origami was formed with only edge staples scaling with the size of the complete structure.
Show more

180 Read more

Self-Assembly Properties of DNA Origami, Gold Nanostructures, and Diblock Compatibilizers.

Self-Assembly Properties of DNA Origami, Gold Nanostructures, and Diblock Compatibilizers.

washed and resuspended in water (solid, blue line). The AuNR longitudinal peak is blue- shifted, indicating partial aggregation..................................................................................... 72 Figure 34. UV-vis absorbance spectroscopy of AuNRs and single-thiol-DNA (solid, blue line) and later, those same AuNRs, fully functionalized with DNA, after NaCl and TAEMg addition to show that the peak position is maintained (green, short dashes). Also shown are AuNRs with dithiol-DNA (red, long dashes), which shows a peak shift and peak broadening, indicating aggregation. ............................................................................................................ 73 Figure 35. Both native CTAB-AuNRs and lipoic-acid AuNRs are aggregated and cannot enter the gel. The thiol-AuNRs migrate into the gel and remain red in color. ....................... 75 Figure 36. EtBr stained agarose gel electrophoresis (1% agarose, 1xTAEMg) of A) DNA- AuNSs, B) Design 1 tetrahedra with excess ssDNA, C) filtered Design 1 tetrahedra, and D) tetrahedra hybridized with AuNSs, in which the AuNSs are in 5x excess of the origami. (Top) White light illuminated image of the gel and (bottom) UV illuminated. ..................... 77 Figure 37. Tall Rectangle origami with AuNSs A) along one edge, and B) along two edges, or C) at each corner. For each of A and B, i) shows a schematic of the desired product, ii) shows AFM images of the samples, and iii) shows SEM images of the samples. For C, i) shows the schematic, ii) shows SEM images, and iii) shows TEM images using the method from Chapter 2....................................................................................................................... 79 Figure 38. A) Tall Rectangle origami with a AuNR on one edge. i) Schematic and ii) SEM images. B) Tall Rectangle origami with a AuNR on each edge. C) Design 1 tetrahedra with a AuNR on an arm, and D) the same but with AuNSs at the vertices. E) A core-satellite
Show more

222 Read more

Rapid self-assembly of DNA on a microfluidic chip

Rapid self-assembly of DNA on a microfluidic chip

of heterozygous samples from the PCR with heterozygous samples after on-chip reassembly. After adding forma- mide, the electropherogram of the first separation analysis following any long injection shows a clearly defined tran- sient peak. For H63D samples the transient peak is a sin- gle peak, whereas for S65C the transient peak is clefted. We have found that the transient peaks vary in size signif- icantly depending upon the electrophoretic and PCR pro- tocols used. Initially we had assumed that this transient peak indicated that the reassembly of the DNA was not 'random' but instead hybridised first in a high-melting point region, and only slowly thereafter. In this model, the presence of the split-peak would provide information upon the location of the mutation. This suggests that mutation S65C is within the higher melting point domain, while the H63D is not. However, as determined by the Meltmap program (generously provided by L. Ler- man (MIT)), neither the H63D nor S65C mutations were within the high melting point region of the exon (data not shown).
Show more

10 Read more

Show all 10000 documents...