DNA and DNAzyme-Mediated 2D Colloidal Assembly

Regulating Spatial Localization and Reactivity Biasness of DNAzymes by Metal Ions and Oligonucleotides

Chemical gradient sensing behavior of catalytically active colloids and enzymes is an area of immense interest owing to their importance in understanding fundamental spatiotemporal complexity pattern in living systems and designing of dynamic materials. Herein, we have shown peroxidase activity of DNAzyme (G-quadruplex-hemin complex tagged in a micron-sized glass bead) can be modulated by metal ions and metal ion-binding oligonucleotides. Next we demonstrated both experimentally and theoretically that the localization and product formation ability of the DNAzyme containing particle remains biased to the more catalytically active zone where concentration of metal ion (Hg2+) inhibitor is low. Interestingly, this biased localization can be broken by introduction of Hg2+ binding oligonucleotide in the system. Additionally, macroscopically asymmetric catalytic product distributed zone has also been achieved on this process, showing possibility in regulation in autonomous spatially controlled chemical process. This demonstration of autonomous modulation of the localization pattern and spatially specific enhanced product forming ability of DNAzymes will further enable in designing of responsive nucleic acid-based motile materials and surfaces.

DNA Assembly-Based Stimuli-Responsive Systems

Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.

Enhanced Porosity in Self-Assembled Morphologies Mediated by Charged Lobes on Patchy Particles

Colloidal patchy particles are particles with anisotropic "patches" decorating their surfaces. Several properties of these patches including their size, number, location, and interactions provide control over self-assembly of patchy particles into structures with desired properties. We report on simulation studies of particles where patches take the form of lobes. Based on the number and locations of lobes, these particles have different shapes (trigonal planar, square planar, tetrahedral, trigonal bipyramidal, and octahedral). We investigated the effect of incorporating charges on the lobes in achieving porous self-assembled morphologies across a range of temperatures. We observed that an increase in the charge on the lobe resulted in lobed particles assembling over a wider range of temperatures. We also observed that the lobed particles with charges self-assembled into structures with enhanced porosity in comparison to lobed particles without charges.

Bioapplications of DNA nanotechnology at the solid-liquid interface

DNA nanotechnology engineered at the solid-liquid interface has advanced our fundamental understanding of DNA hybridization kinetics and facilitated the design of improved biosensing, bioimaging and therapeutic platforms. Three research branches of DNA nanotechnology exist: (i) structural DNA nanotechnology for the construction of various nanoscale patterns; (ii) dynamic DNA nanotechnology for the operation of nanodevices; and (iii) functional DNA nanotechnology for the exploration of new DNA functions. Although the initial stages of DNA nanotechnology research began in aqueous solution, current research efforts have shifted to solid-liquid interfaces. Based on shape and component features, these interfaces can be classified as flat interfaces, nanoparticle interfaces, and soft interfaces of DNA origami and cell membranes. This review briefly discusses the development of DNA nanotechnology. We then highlight the important roles of structural DNA nanotechnology in tailoring the properties of flat interfaces and modifications of nanoparticle interfaces, and extensively review their successful bioapplications. In addition, engineering advances in DNA nanodevices at interfaces for improved biosensing both in vitro and in vivo are presented. The use of DNA nanotechnology as a tool to engineer cell membranes to reveal protein levels and cell behavior is also discussed. Finally, we present challenges and an outlook for this emerging field.

Binary Superlattice Design by Controlling DNA-Mediated Interactions

Most binary superlattices created using DNA functionalization rely on particle size differences to achieve compositional order and structural diversity. Here we study two-dimensional (2D) assembly of DNA-functionalized micron-sized particles (DFPs), and employ a strategy that leverages the tunable disparity in interparticle interactions, and thus enthalpic driving forces, to open new avenues for design of binary superlattices that do not rely on the ability to tune particle size (i.e., entropic driving forces). Our strategy employs tailored blends of complementary strands of ssDNA to control interparticle interactions between micron-sized silica particles in a binary mixture to create compositionally diverse 2D lattices. We show that the particle arrangement can be further controlled by changing the stoichiometry of the binary mixture in certain cases. With this approach, we demonstrate the ability to program the particle assembly into square, pentagonal, and hexagonal lattices. In addition, different particle types can be compositionally ordered in square checkerboard and hexagonal-alternating string, honeycomb, and Kagome arrangements.

Speeding up the self-assembly of a DNA nanodevice using a variety of polar solvents

The specific recognition and programmable assembly properties make DNA a potential material for nanodevices. However, the more intelligent the nanodevice is, the more complicated the structure of the nanodevice is, which limits the speed of DNA assembly. Herein, to address this problem, we investigate the performance of DNA Strand Displacement Reaction (DSDR) in a mixture of polar organic solvents and aqueous buffer and demonstrate that the organic polar solvent can speed up DNA self-assembly efficiently. Taking DSDR in 20% ethanol as an example, first we have demonstrated that the DSDR is highly accelerated in the beginning of the reaction and it can complete 60% of replacement reactions (160% enhancement compared with aqueous buffer) in the first 300 seconds. Secondly, we calculated that the ΔΔG of the DSDR in 20% ethanol (-18.2 kcal mol(-1)) is lower than that in pure aqueous buffer (-32.6 kcal mol(-1)), while the activation energy is lowered by introducing ethanol. Finally, we proved that the DSDR on the electrode surface can also be accelerated using this simple strategy. More importantly, to test the efficacy of this approach in nanodevices with a complicated and slow DNA self-assembly process, we apply this strategy in the hybridization chain reaction (HCR) and prove the acceleration is fairly obvious in 20% ethanol, which demonstrates the feasibility of the proposed strategy in DNA nanotechnology and DNA-based biosensors.

Adsorbed films of three-patch colloids: continuous and discontinuous transitions between thick and thin films

We investigate numerically the role of spatial arrangement of the patches on the irreversible adsorption of patchy colloids on a substrate. We consider spherical three-patch colloids and study the dependence of the kinetics on the opening angle between patches. We show that growth is suppressed below and above minimum and maximum opening angles, revealing two absorbing phase transitions between thick and thin film regimes. While the transition at the minimum angle is continuous, in the directed percolation class, that at the maximum angle is clearly discontinuous. For intermediate values of the opening angle, a rough colloidal network in the Kardar-Parisi-Zhang universality class grows indefinitely. The nature of the transitions was analyzed in detail by considering bond flexibility, defined as the dispersion of the angle between the bond and the center of the patch. For the range of flexibilities considered we always observe two phase transitions. However, the range of opening angles where growth is sustained increases with flexibility. At a tricritical flexibility, the discontinuous transition becomes continuous. The practical implications of our findings and the relation to other nonequilibrium transitions are discussed.

Dumbbells, trikes and quads: organic-inorganic hybrid nanoarchitectures based on "clicked" gold nanoparticles

The controlled assembly of gold nanoparticles in terms of the spatial arrangement and number of particles is essential for many future applications like electronic devices, sensors and labeling. Here an approach is presented to build up oligomers of mono functionalized gold nanoparticles by the use of 1,3-bipolar azide alkyne cycloaddition click chemistry. The gold nanoparticles of 1.3 nm diameter are stabilized by one dendritic thioether ligand comprising an alkyne function. Together with di-, tri- and tetra-azide linker molecules the gold nanoparticle can be covalently coupled by a wet chemical protocol. The reaction is tracked with IR and UV-vis spectroscopy and the yielded organic-inorganic hybrid structures are analyzed by transmission electron microscopy. To evaluate the success of this click chemistry reaction statistical analysis of the formed oligomers is performed. The geometric and spatial arrangements of the found oligomers match perfectly the calculated values for the used linker molecules. Dimers, trimers and tetramers could be identified after the reaction with the corresponding linker molecule. The results of this model reaction suggest that the used click chemistry protocol is working well with mono functionalized gold nanoparticles.

Tunable assembly of colloidal crystal alloys using magnetic nanoparticle fluids

We demonstrate a magnetic technique for assembling bidisperse and tridisperse colloidal particle fluids into a variety of complex structures with dimensionality ranging from 0-D (rings) to 1-D (chains) to 2-D (tiles). Compared with prior work on bidisperse particles that are commensurate in size, here we explore the assembly of different sized particles, and we show that due to packing constraints, new particle structures can be realized experimentally. Extending these experiments to a tridisperse system, we demonstrate that at low concentrations the smallest particle does not change the underlying crystal structures of the bidisperse system; however, it can assist in the formation of crystallite structures that were not stable in a bidisperse system. Additionally, we discovered that the smallest particle mimics the role of the ferrofluid, by shifting the locations in phase space where the bidisperse crystal structures can be experimentally obtained. Finally, we demonstrate that 3-particle crystal structures can be tuned by varying the strength of the external field, which is not possible in a 2-particle system.

Direct control of the spatial arrangement of gold nanoparticles in organic-inorganic hybrid superstructures

The directed assembly of gold nanoparticles is essential for their use in many kinds of applications, such as electronic devices, biological labels, and sensors. Herein an atomic alteration in the molecular structure of ligand-stabilized gold nanoparticles that can shift the interparticle distance up to 1 nm upon covalent coupling to organic-inorganic superstructures is presented. Gold nanoparticles are stabilized by two octadentate thioether ligands and have a mean diameter of 1.1 nm. The ligands contain a central rigid rod varying in length and terminally functionalized with a protected acetylene. The two peripheral functional groups on each particle enable the directed assembly of nanoparticles to dimers, trimers, and tetramers by oxidative acetylene coupling. This is a wet chemical protocol resulting in covalently bound nanoparticles. These organic-inorganic hybrid superstructures are analyzed by transmission electron microscopy, small angle X-ray scattering, and UV/vis spectroscopy. The focus of the comparison here is the subunit, which is anchoring the bridgehead, either a pyridine or benzene moiety. The pyridine-based ligands reflect the calculated length of the rigid-rod spacer in their interparticle distances in the obtained hybrid structures. This suggests a perpendicular arrangement that results from the coordination of the pyridine's lone pair to the gold surface. An atomic variation in the ligand's center leads to smaller interparticle distances in the case of hybrid structures obtained from benzene ligands. This large difference in the spatial arrangement suggests a tangential arrangement of the interparticle bridging structure in the latter case. Consequently a rather flat arrangement parallel to the particle surface must be assumed for the central benzene unit of the benzene-based ligand.

DNA-based soft phases

This chapter reviews the state-of-the-art in the study of molecular or colloidal systems whose mutual interactions are mediated by DNA molecules. In the last decade, the robust current knowledge of DNA interactions has enabled an impressive growth of self-assembled DNA-based structures that depend crucially on the properties of DNA-DNA interactions. In many cases, structures are built on design by exploiting the programmable selectivity of DNA interactions and the modularity of their strength. The study of DNA-based materials is definitely an emerging field in condensed matter physics, nanotechnology, and material science. This chapter will consider both systems that are entirely constructed by DNA and hybrid systems in which latex or metal colloidal particles are coated by DNA strands. We will confine our discussion to systems in which DNA-mediated interactions promote the formation of "phases," that is structures extending on length scales much larger than the building blocks. Their self-assembly typically involves a large number of interacting particles and often features hierarchical stages of structuring. Because of the possibility of fine-tuning the geometry and strength of the DNA-mediated interactions, these systems are characterized by a wide variety of patterns of self-assembly, ranging from amorphous, to liquid crystalline, to crystalline in one, two, or three dimensions.

Recent advances in DNA-based directed assembly on surfaces

In the last decade, "small" and "integrated" have been keywords in the field of device fabrication as the desire to exploit nanoscale phenomena and make electronic, photonic and magnetic arrays has grown. In an effort to improve resolution and control costs, much work has been dedicated to developing alternatives to conventional microfabrication technology. For this purpose, biomolecular assembly and DNA nanotechnology in particular are appealing owing to their inherent size and capacity for molecular recognition. Herein, we review recent achievements in DNA-based directed assembly on substrates. These include novel methods for patterning and depositing nanomaterials on DNA-modified surfaces as well as using synthetic DNA nanostructures such as DNA tiles and origami as templates to direct the assembly of nanoscale components. Particular attention is paid to integrating self-assembly with top-down lithography, and some possible directions for future work are discussed.

Colloidal self-assembly meets nanofabrication: from two-dimensional colloidal crystals to nanostructure arrays

Self-assembly of colloidal microspheres or nanospheres is an effective strategy for fabrication of ordered nanostructures. By combination of colloidal self-assembly with nanofabrication techniques, two-dimensional (2D) colloidal crystals have been employed as masks or templates for evaporation, deposition, etching, and imprinting, etc. These methods are defined as "colloidal lithography", which is now recognized as a facile, inexpensive, and repeatable nanofabrication technique. This paper presents an overview of 2D colloidal crystals and nanostructure arrays fabricated by colloidal lithography. First, different methods for fabricating self-assembled 2D colloidal crystals and complex 2D colloidal crystal structures are summarized. After that, according to the nanofabrication strategy employed in colloidal lithography, related works are reviewed as colloidal-crystal-assisted evaporation, deposition, etching, imprinting, and dewetting, respectively.

Aggregation-disaggregation transition of DNA-coated colloids: experiments and theory

Colloids coated with complementary single-stranded DNA "sticky ends" associate and dissociate upon heating. Recently, microscopy experiments have been carried out where this association-dissociation transition has been investigated for different types of DNA and different DNA coverages [R. Dreyfus, M. E. Leunissen, R. Sha, A. V. Tkachenko, N. C. Seeman, D. J. Pine, and P. M. Chaikin, Phys. Rev. Lett. 102, 048301 (2009)]. It has been shown that this transition can be described by a simple quantitative model which takes into account the features of the tethered DNA on the particles and unravels the importance of an entropy cost due to DNA confinement between the surfaces. In this paper, we first present an extensive description of the experiments that were carried out. A step-by-step model is then developed starting from the level of statistical mechanics of tethered DNA to that of colloidal aggregates. This model is shown to describe the experiments with excellent agreement for the temperature and width of the transition, which are both essential properties for complex self-assembly processes.

Nano-flares for mRNA regulation and detection

We build off the previously described concept of a nanoflare to develop an oligonucleotide gold nanoparticle conjugate that is capable of both detecting and regulating intracellular levels of mRNA. We characterize the binding rate and specificity of these materials using survivin, a gene associated with the diagnosis and treatment of cancer, as a target. The nanoconjugate enters cells and binds mRNA, thereby decreasing the relative abundance of mRNA in a dose- and sequence-dependent manner, resulting in a fluorescent response. This represents the first demonstration of a single material capable of both mRNA regulation and detection. Further, we investigate the intracellular biochemistry of the nanoconjugate, elucidating its mechanism of gene regulation. This work is important to the study of biologically active nanomaterials such as the nanoflare and is a first step toward the development of an mRNA responsive "theranostic".

Effect of nanoparticle concentration on the convective deposition of binary suspensions

We investigate the coupling between the suspension properties and the deposition process during convective deposition of aqueous binary suspensions of 1 microm silica microspheres and 100 nm polystyrene (PS) nanoparticles. The structures formed from this rapid and scalable process have use in a variety of optical, chemical, and biochemical sensing applications. At conditions that produce a well-ordered microsphere monolayer at a silica volume fraction of 20% in the absence of nanoparticles, we examine the effect of varying the concentration of nanoparticles from 0% to 16% on the quality of the microsphere deposition and the exposure of the microspheres within the PS layer. At low concentrations of nanoparticles, the deposition results in an instability that forms stripes parallel to the receding contact line. Optimum deposition occurs between 6% and 8% PS and forms a monolayer having the same high degree of uniformity as the monodisperse suspension is fabricated. For higher concentrations, the deposition is increasingly less uniform as a result of nanoparticle depletion destabilizing the microspheres. The degree to which each microsphere is buried by the nanoparticles in the deposited thin film increases with nanoparticle concentration. This variation in coverage also suggests interplay between deposition and nanoparticle engineered properties of the suspension that influence the deposited morphology.

Simple quantitative model for the reversible association of DNA coated colloids

We investigate the reversible association of micrometer-sized colloids coated with complementary single-stranded DNA "sticky ends" as a function of the temperature and the sticky end coverage. We find that even a qualitative description of the dissociation transition curves requires the inclusion of an entropic cost. We develop a simple general model for this cost in terms of the configurational entropy loss due to binding and confinement of the tethered DNA between neighboring particles. With this easy-to-use model, we demonstrate for different kinds of DNA constructs quantitative control over the dissociation temperature and the sharpness of the dissociation curve, both essential properties for complex self-assembly processes.

Beyond molecular recognition: using a repulsive field to tune interfacial valency and binding specificity between adhesive surfaces

Surface-bound biomolecular fragments enable "smart" materials to recognize cells and other particles in applications ranging from tissue engineering and medical diagnostics to colloidal and nanoparticle assembly. Such smart surfaces are, however, limited in their design to biomolecular selectivity. This feature article demonstrates, using a completely nonbiological model system, how specificity can be achieved for particle (and cell) binding, employing surface designs where immobilized nanoscale adhesion elements are entirely nonselective. Fundamental principles are illustrated by a model experimental system where 11 nm cationic nanoparticles on a planar negative silica surface interact with flowing negative silica microspheres having 1.0 and 0.5 microm diameters. In these systems, the interfacial valency, defined as the number of cross-bonds needed to capture flowing particles, is tunable through ionic strength, which alters the range of the background repulsion and therefore the effective binding strength of the adhesive elements themselves. At high ionic strengths where long-range electrostatic repulsions are screened, single surface-bound nanoparticles capture microspheres, defining the univalent regime. At low ionic strengths, competing repulsions weaken the effective nanoparticle adhesion so that multiple nanoparticles are needed for microparticle capture. This article discusses important features of the univalent regime and then illustrates how multivalency produces interfacial-scale selectivity. The arguments are then generalized, providing a possible explanation for highly specific cell binding in nature, despite the degeneracy of adhesion molecules and cell types. The mechanism for the valency-related selectivity is further developed in the context of selective flocculation in the colloidal literature. Finally, results for multivalent binding are contrasted with the current thinking for interfacial design and the presentation of adhesion moieties on engineered surfaces.