We examine the crystallization dynamics of nanoparticles reversibly tethered by DNA hybridization. We show that the crystallization happens readily only in a narrow temperature "slot," and always proceeds via a two-step process, mediated by a highly-connected amorphous intermediate. For lower temperature quenches, the dynamics of unzipping strands in the amorphous state is sufficiently slow that crystallization is kinetically hindered. This accounts for the well-documented difficulty of forming crystals in these systems. The strong parallel to the crystallization behavior of proteins and colloids suggests that these disparate systems crystallize in an apparently universal manner.
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure. Depending on the geometry and the size of the particles, the grafting density of the ssDNA chains, and the length and choice of DNA sequences, a number of different crystalline structures can be fabricated. However, understanding how these factors contribute synergistically to the self-assembly process of DNA-functionalized nano- or micro-sized particles remain…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered crystalline assemblies, and instead, disordered structures start to form when the chain length exceeds a certain threshold, which is consistent with the previous experiments. Further analysis of the simulation data suggests weakening interparticle interactions with increasing chain length, thereby shifting the suitable assembly conditions to lower temperatures …
DNA-coated colloids can self-assemble into an incredible diversity of crystal structures, but applications of this technology are limited by poor understanding and control over the dynamical crystallization pathways. To address this challenge, we use microfluidics to quantify the self-assembly dynamics of DNA-programmed colloidal crystals, from thermally-activated nucleation through reaction-limited and diffusion-limited phases of crystal growth. Our detailed measurements of the temperature and concentration dependence of the kinetics at all stages along the crystallization pathway provide a s…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized part…
We present a coarse-grained model of DNA-functionalized colloids that is computationally tractable. Importantly, the model parameters are solely based on experimental data. Using this highly simplified model, we can predict the phase behavior of DNA-functionalized nano-colloids without assuming pairwise additivity of the inter-colloidal interactions. Our simulations show that for nano-colloids, the assumption of pairwise additivity leads to substantial errors in the estimate of the free energy of the crystal phase. We compare our results with available experimental data and find that the simul…
Atomistic molecular dynamics simulations have been carried out to reveal the characteristic features of ethylenediamine (EDA) cored protonated poly amido amine (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) that are functionalized with single stranded DNAs (ssDNAs). The four ssDNA strands that are attached via alkythiolate [-S (CH2)6-] linker molecule to the free amine groups on the surface of the PAMAM dendrimers observed to undergo a rapid conformational change during the 25 ns long simulation period. From the RMSD values of ssDNAs, we find relative stability in the case of purine rich s…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4] of a large number of individuals are crucial for the analysis of mutations [5] and hereditary diseases, paving the way to preventive medicine [6]. DNA sequencing is, however, currently still a vastly time-consuming and very expensive task [4], consisting of pre-processing steps, the actual sequencing using the Sanger method, and post-processing in the form …
Many industrial soft materials often include oil-in-water (O/W) emulsions at the core of their formulations. By using tuneable interface stabilizing agents, such emulsions can self-assemble into complex structures. DNA has been used for decades as a thermoresponsive highly specific binding agent between hard and, recently, soft colloids. Up until now, emulsion droplets functionalized with DNA had relatively low coating densities and were expensive to scale up. Here a general O/W DNA-coating method using functional non-ionic amphiphilic block copolymers, both diblock and triblock, is presented.…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since hybridization of double strands will only occur if the base sequences of single strands are complementary. Nanoparticles and colloids functionalized by four single strands of DNA can be thought of as designed analogs to tetrahedral network forming atoms and molecules, with a difference that the attached DNA strands allow for control of the length scale of bonding rela…
We study the problem of the self-assembly of nanoparticles (NPs) into finite mesoscopic structures with a programmed local morphology and complex overall shape. Our proposed building blocks are NPs directionally-functionalized with DNA. The combination of directionality and selectivity of interactions allows one to avoid unwanted metastable configurations which have been shown to lead to slow self-assembly kinetics even in much simpler systems. With numerical simulations, we show that a variety of target mesoscopic objects can be designed and self-assembled in near perfect yield. They include …
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder model of shear unzipping proposed earlier by deGennes [deGennes P. G. C. R. Acad. Sci., Ser. IV; Phys., Astrophys. 2001, 1505]. Using this model and a combination of analytical and numerical methods, we study the DNA "unzipping" transition when the shearing force exceeds a critical threshold at zero temperature. We also explore the effects of sequence heteroge…
Under prolonged starvation, the nucleoid of E. coli bacteria forms nanocrystalline complexes with the protein Dps. By one hypothesis, this effect is considered to be a manifestation of a general strategy of self-preservation of living organisms under adverse conditions by forming stable ordered structures which do not require consumption of energy for maintaining the order. The effect of nucleoid biocrystallization in starved bacteria has been investigated in a number of studies using electron microscopy. However, this method did not answer all questions regarding the structure of the nanocrys…
Limited bonding valence, usually accompanied by well-defined directional interactions and selective bonding mechanisms, is nowadays considered among the key ingredients to create complex structures with tailored properties: even though isotropically interacting units already guarantee access to a vast range of functional materials, anisotropic interactions can provide extra instructions to steer the assembly of specific architectures. The anisotropy of effective interactions gives rise to a wealth of self-assembled structures both in the realm of suitably synthesized nano- and micro-sized buil…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors and nanoparticle based drug delivery platforms. In Chapter I we introduce the system, which generically consists of colloidal particles functionalized with specially designed DNA markers. The sequence of bases on the DNA markers determines the particle type. Due to the hybridization between complementary single-stranded DNA, specific, type-dependent interac…
We propose a new strategy to improve the self-assembly properties of DNA-functionalised colloids. The problem that we address is that DNA-functionalised colloids typically crystallize in a narrow temperature window, if at all. The underlying reason is the extreme sensitivity of DNA-mediated interactions to temperature or other physical control parameters. We propose to widen the window for colloidal crystallization by exploiting the competition between DNA linkages with different nucleotide sequences, which results in a temperature-dependent switching of the dominant bond type. Following such …
DNA-driven self-assembly enables precise positioning of the colloidal nanoparticles owing to specific Watson-Crick interactions. Another important feature of this self-assembly method is its reversibility by controlling the temperature of the medium. In this work, we study the potential of another mechanism to control binding/unbinding process of the DNA-functionalized gold nanoparticles. We employ the laser radiation that can be absorbed by the gold nanoparticles to heat their network and disassociate it. Here, we show that we can actively control the optical properties of the nanoparticle ne…
