Engineering Ultrasoft Interactions in Stiff All-DNA Dendrimers by Site-Specific Control of Scaffold Flexibility.

A combined experimental and theoretical study of the structural correlations in moderately concentrated suspensions of all-DNA dendrimers of the second generation (G2) with controlled scaffold rigidity is reported here. Small-angle X-ray scattering experiments in concentrated aqueous saline solutions of stiff all-DNA G2 dendritic constructs reveal a novel anomalous liquid-like phase behavior which is reflected in the calculated structure factors as a two-step increase at low scattering wave vectors. By developing a new design strategy for adjusting the particle's internal flexibility based on site-selective incorporation of single-stranded DNA linkers into the dendritic scaffold, it is shown that this unconventional type of self-organization is strongly contingent on the dendrimer's stiffness. A comprehensive computer simulation study employing dendritic models with different levels of coarse-graining, and two theoretical approaches based on effective, pair-potential interactions, remarkably confirmed the origin of this unusual liquid-like behavior. The results demonstrate that the precise control of the internal structure of the dendritic scaffold conferred by the DNA can be potentially used to engineer a rich palette of novel ultrasoft interaction potentials that could offer a route for directed self-assembly of intriguing soft matter phases and experimental realizations of a host of unusual phenomena theoretically predicted for ultrasoft interacting systems.

Blunt-End Driven Re-entrant Ordering in Quasi Two-Dimensional Dispersions of Spherical DNA Brushes.

We investigate the effects of crowding on the conformations and assembly of confined, highly charged, and thick polyelectrolyte brushes in the osmotic regime. Particle tracking experiments on increasingly dense suspensions of colloids coated with ultralong double-stranded DNA (dsDNA) fragments reveal nonmonotonic particle shrinking, aggregation, and re-entrant ordering. Theory and simulations show that aggregation and re-entrant ordering arise from the combined effect of shrinking, which is induced by the osmotic pressure exerted by the counterions absorbed in neighbor brushes and of a short-range attractive interaction competing with electrostatic repulsion. An unconventional mechanism gives origin to the short-range attraction: blunt-end interactions between stretched dsDNA fragments of neighboring brushes, which become sufficiently intense for dense and packed brushes. The attraction can be tuned by inducing free-end backfolding through the addition of monovalent salt. Our results show that base stacking is a mode parallel to hybridization to steer colloidal assembly in which attractions can be fine-tuned through salinity and, potentially, grafting density and temperature.

Self-Assembly of All-DNA Rods with Controlled Patchiness.

Double-stranded DNA (dsDNA) fragments exhibit noncovalent attractive interactions between their tips. It is still unclear how DNA liquid crystal self-assembly is affected by such blunt-end attractions. It is demonstrated that stiff dsDNA fragments with moderate aspect ratio can specifically self-assemble in concentrated aqueous solutions into different types of smectic mesophases on the basis of selectively screening of blunt-end DNA stacking interactions. To this end, this type of attractions are engineered at the molecular level by constructing DNA duplexes where the attractions between one or both ends are screened by short hairpin caps. All-DNA bilayer and monolayer smectic-A type of phases, as well as a columnar phase, can be stabilized by controlling attractions strength. The results imply that the so far elusive smectic-A in DNA rod-like liquid crystals is a thermodynamically stable phase. The existence of the bilayer smectic phase is confirmed by Monte-Carlo simulations of hard cylinders decorated with one attractive terminal site. This work demonstrates that DNA blunt-ends behave as well-defined monovalent attractive patches whose strength and position can be potentially precisely tuned, highlighting unique opportunities concerning the stabilization of nonconventional DNA-based lyotropic liquid crystal phases assembled by all-DNA patchy particles with arbitrary geometry and composition.

Self assembling cluster crystals from DNA based dendritic nanostructures.

Cluster crystals are periodic structures with lattice sites occupied by several, overlapping building blocks, featuring fluctuating site occupancy, whose expectation value depends on thermodynamic conditions. Their assembly from atomic or mesoscopic units is long-sought-after, but its experimental realization still remains elusive. Here, we show the existence of well-controlled soft matter cluster crystals. We fabricate dendritic-linear-dendritic triblock composed of a thermosensitive water-soluble polymer and nanometer-scale all-DNA dendrons of the first and second generation. Conclusive small-angle X-ray scattering (SAXS) evidence reveals that solutions of these triblock at sufficiently high concentrations undergo a reversible phase transition from a cluster fluid to a body-centered cubic (BCC) cluster crystal with density-independent lattice spacing, through alteration of temperature. Moreover, a rich concentration-temperature phase diagram demonstrates the emergence of various ordered nanostructures, including BCC cluster crystals, birefringent cluster crystals, as well as hexagonal phases and cluster glass-like kinetically arrested states at high densities.

DNA Self-Assembly Mediated by Programmable Soft-Patchy Interactions.

Adding shape and interaction anisotropy to a colloidal particle offers exquisitely tunable routes to engineer a rich assortment of complex-architected structures. Inspired by the hierarchical self-assembly concept with block copolymers and DNA liquid crystals and exploiting the unique assembly properties of DNA, we report here the construction and self-assembly of DNA-based soft-patchy anisotropic particles with a high degree of modularity in the system's design. By programmable positioning of thermoresponsive polymeric patches on the backbone of a stiff DNA duplex with linear and star-shaped architecture, we reversibly drive the DNA from a disordered ensemble to a diverse array of long-range ordered multidimensional nanostructures with tunable lattice spacing, ranging from lamellar to bicontinuous double-gyroid and double-diamond cubic morphologies, through the alteration of temperature. Our results demonstrate that the proposed hierarchical self-assembly strategy can be applied to any kind of DNA nanoarchitecture, highlighting the design principles for integration of self-assembly concepts from the physics of liquid crystals, block copolymers, and patchy colloids into the continuously growing interdisciplinary research field of structural DNA nanotechnology.

Model-Free Rheo-AFM Probes the Viscoelasticity of Tunable DNA Soft Colloids.

Atomic force microscopy rheological measurements (Rheo-AFM) of the linear viscoelastic properties of single, charged colloids having a star-like architecture with a hard core and an extended, deformable double-stranded DNA (dsDNA) corona dispersed in aqueous saline solutions are reported. This is achieved by analyzing indentation and relaxation experiments performed on individual colloidal particles by means of a novel model-free Fourier transform method that allows a direct evaluation of the frequency-dependent linear viscoelastic moduli of the system under investigation. The method provides results that are consistent with those obtained via a conventional fitting procedure of the force-relaxation curves based on a modified Maxwell model. The outcomes show a pronounced softening of the dsDNA colloids, which is described by an exponential decay of both the Young's and the storage modulus as a function of the salt concentration within the dispersing medium. The strong softening is related to a critical reduction of the size of the dsDNA corona, down to ≈70% of its size in a salt-free solution. This can be correlated to significant topological changes of the dense star-like polyelectrolyte forming the corona, which are induced by variations in the density profile of the counterions. Similarly, a significant reduction of the stiffness is obtained by increasing the length of the dsDNA chains, which we attribute to a reduction of the DNA density in the outer region of the corona.

Structure and stimuli-responsiveness of all-DNA dendrimers: theory and experiment.

We present a comprehensive theoretical and experimental study of the solution phase properties of a DNA-based family of nanoparticles - dendrimer-like DNA molecules (DL-DNA). These charged DNA dendrimers are novel macromolecular aggregates, which hold high promise in targeted self-assembly of soft matter systems in the bulk and at interfaces. To describe the behaviour of this family of dendrimers (with generations ranging from G1 to G7), we use a theoretical model in which base-pairs of a single DL-DNA molecule are modeled by charged monomers, whose interactions are chosen to mimic the equilibrium properties of DNA correctly. Experimental results on the sizes and conformations of DL-DNA are based on static and dynamic light scattering; and molecular dynamics simulations are employed to model the equilibrium properties of DL-DNA, which compare favorably to the findings from experiments while at the same time providing a host of additional information and insight into the molecular structure of the nanostructures. We also examine the salt-responsiveness of these macromolecules, finding that despite the strong screening of electrostatic interactions brought about by the added salt, the macromolecules shrink only slightly, their size robustness stemming from the high bending rigidity of the DNA-segments. The study of these charged dendrimer systems is an important field of research in the area of soft matter due to their potential role for various interdisciplinary applications, ranging from molecular cages and carriers for drug delivery in a living organism to the development of dendrimer- and dendron-based ultra-thin films in the area of nanotechnology. These findings are essential to determine if DL-DNA is a viable candidate for the experimental realization of cluster crystals in the bulk, a novel form of solid with multiple site occupancy.

Smectic phase in suspensions of gapped DNA duplexes.

Smectic ordering in aqueous solutions of monodisperse stiff double-stranded DNA fragments is known not to occur, despite the fact that these systems exhibit both chiral nematic and columnar mesophases. Here, we show, unambiguously, that a smectic-A type of phase is formed by increasing the DNA's flexibility through the introduction of an unpaired single-stranded DNA spacer in the middle of each duplex. This is unusual for a lyotropic system, where flexibility typically destabilizes the smectic phase. We also report on simulations suggesting that the gapped duplexes (resembling chain-sticks) attain a folded conformation in the smectic layers, and argue that this layer structure, which we designate as smectic-fA phase, is thermodynamically stabilized by both entropic and energetic contributions to the system's free energy. Our results demonstrate that DNA as a building block offers an exquisitely tunable means to engineer a potentially rich assortment of lyotropic liquid crystals.

Direct visualization of conformation and dense packing of DNA-based soft colloids.

Soft colloids--such as polymer-coated particles, star polymers, block-copolymer micelles, microgels--constitute a broad class of materials where microscopic properties such as deformability and penetrability of the particle play a key role in tailoring their macroscopic properties which is of interest in many technological areas. The ability to access these microscopic properties is not yet demonstrated despite its great importance. Here we introduce novel DNA-coated colloids with star-shaped architecture that allows accessing the above local structural information by directly visualizing their intramolecular monomer density profile and arm's free-end locations with confocal fluorescent microscopy. Compression experiments on a two-dimensional hexagonal lattice formed by these macromolecular assemblies reveal an exceptional resistance to mutual interpenetration of their charged corona at pressures approaching the MPa range. Furthermore, we find that this lattice, in a close packing configuration, is surprisingly tolerant to particle size variation. We anticipate that these stimuli-responsive materials could aid to get deeper insight in a wide range of problems in soft matter, including the study and design of biomimetic lubricated surfaces.