Reversible self-assembly and directed assembly of DNA-linked micrometer-sized colloids

If a solution of DNA-coated nanoparticles is allowed to crystallize, the thermodynamic structure can be predicted by a set of structural design rules analogous to Pauling's rules for ionic crystallization. The details of the crystallization process, however, have proved more difficult to characterize as they depend on a complex interplay of many factors. Here, we report that this crystallization process is dictated by the individual DNA bonds and that the effect of changing structural or environmental conditions can be understood by considering the effect of these parameters on free oligonucleotides. Specifically, we observed the reorganization of nanoparticle superlattices using time-resolved synchrotron small-angle X-ray scattering in systems with different DNA sequences, salt concentrations, and densities of DNA linkers on the surface of the nanoparticles. The agreement between bulk crystallization and the behavior of free oligonucleotides may bear important consequences for constructing novel classes of crystals and incorporating new interparticle bonds in a rational manner.DNA materials | self assembly | nanostructure M aterials scientists have accomplished much by studying the way atoms and molecules crystallize. In these systems, however, the identity of the atom and its bonding behavior cannot be independently controlled, limiting our ability to tune material properties at will. In contrast, when a nanoparticle is modified with a dense shell of upright, oriented DNA, it can behave as a programmable atom equivalent (PAE) (1, 2) that can be used to synthesize diverse crystal structures with independent control over composition, scale, and lattice symmetry (3-14). The thermodynamic product of this crystallization process has been extensively studied by both experimental and theoretical means, and thus a series of design rules has been proposed and validated with a simple geometric model known as the complementary contact model (CCM). These rules allow one to predict the thermodynamically favored structure as the arrangement of particles that maximizes complementary contacts and therefore DNA hybridization (2, 6). These efforts have been very successful in predicting the thermodynamically favored product; recent studies have even demonstrated that PAEs can form single-crystal Wulff polyhedra that are analogous to those formed in atomic systems with the same crystallographic symmetry (15). However, the fact that there is a crystalline thermodynamic product does not mean that any choice of DNA and nanoparticles will result in crystalline systems in practice (3, 4). For example, crystallization has been observed for a relatively narrow class of PAEs (16) and in a manner that is primarily dependent upon the length of the DNA linker and temperature at which assembly occurs (8). Thus, absent from our understanding of these systems is a connection between the crystallization process and the properties of the DNA bonds that form the foundation of these structures.Here, we study the crystallization process and find t...

Section: Discussionmentioning

confidence: 97%

mentioning

confidence: 99%

Importance of the DNA “bond” in programmable nanoparticle crystallization

Macfarlane

Thaner

Brown

et al. 2014

“…Use has also been made of different particles, A and B, functionalized with cDNA strands (13). This configuration, where A-A and B-B bonds do not occur but A-B bonds do (14)(15)(16), has been exploited to form more complex crystals, such as BCC or CsCl structures (12,17). Over the past several years, there has been a great deal of progress in modeling the DNA-mediated interparticle interaction and making quantitative comparisons with experiments (16,(18)(19)(20)(21)(22)(23).…”

Section: Multifunctional | Thermodynamicsmentioning

confidence: 99%

Polygamous particles

Feng

Sha

et al. 2012

Self Cite

DNA is increasingly used as an important tool in programming the self-assembly of micrometer-and nanometer-scale particles. This is largely due to the highly specific thermoreversible interaction of cDNA strands, which, when placed on different particles, have been used to bind precise pairs in aggregates and crystals. However, DNA functionalized particles will only reach their true potential for particle assembly when each particle can address and bind to many different kinds of particles. Indeed, specifying all bonds can force a particular designed structure. In this paper, we present the design rules for multiflavored particles and show that a single particle, DNA functionalized with many different "flavors," can recognize and bind specifically to many different partners. We investigate the cost of increasing the number of flavors in terms of the reduction in binding energy and melting temperature. We find that a single 2-μm colloidal particle can bind to 40 different types of particles in an easily accessible time and temperature regime. The practical limit of ∼100 is set by entropic costs for particles to align complementary pairs and, surprisingly, by the limited number of distinct "useful" DNA sequences that prohibit subunits with nonspecific binding. For our 11 base "sticky ends," the limit is 73 distinct sequences with no unwanted overlaps of 5 bp or more. As an example of phenomena enabled by polygamous particles, we demonstrate a three-particle system that forms a fluid of isolated clusters when cooled slowly and an elastic gel network when quenched. multifunctional | thermodynamicsA defining feature of DNA nanotechnology is the ability of DNA single strands to bind selectively only with complementary strands (1-8). Identical particles coated with identical DNA strands can be joined together by adding to the suspension a linker strand that attaches to the two coatings (9, 10). Such structures have been used for immunoassays (11), particle aggregation, and formation of crystalline structures, typically Face Centered Cubic (FCC) (12). Use has also been made of different particles, A and B, functionalized with cDNA strands (13). This configuration, where A-A and B-B bonds do not occur but A-B bonds do (14-16), has been exploited to form more complex crystals, such as BCC or CsCl structures (12,17). Over the past several years, there has been a great deal of progress in modeling the DNA-mediated interparticle interaction and making quantitative comparisons with experiments (16,(18)(19)(20)(21)(22)(23). Although nanoscale particles are typically coated with tens to hundreds of DNA molecules, and micrometer-scale colloids can be coated with 10 4 -10 5 DNA strands, there has been little work on coating particles with more than one type of DNA sequence on the same particle. Allowing these particles to be "polygamous," to specifically bind to a particular set of other particles, enables not only the fabrication of more complex crystals but the design of more general programmed structures. For rigid structures,...

“…Several groups have reported interaction models (9,(11)(12)(13)(14)(15), all based on capturing the entropic contributions and hybridization thermodynamics of individual grafted DNA molecules. While these models qualitatively describe the existing interaction measurements based on the temperature-dependent aggregation-disaggregation transition of DNA-labeled nanoparticles (16), microparticles (12,14,(17)(18)(19), and polymers (20), or direct measurements with optical tweezers (9), they typically overpredict the interaction strength by roughly two orders of magnitude, corresponding to an unexpectedly large hybridization free energy difference of ∼5 k B T per DNA bridge. Moreover, while the models predict that the interaction strength varies exponentially with temperature, they overestimate the steepness of the temperature dependence by roughly a factor of two.…”

mentioning

confidence: 99%

Direct measurements of DNA-mediated colloidal interactions and their quantitative modeling

Rogers

Crocker

2011

Self Cite

172

210

DNA bridging can be used to induce specific attractions between small particles, providing a highly versatile approach to creating unique particle-based materials having a variety of periodic structures. Surprisingly, given the fact that the thermodynamics of DNA strands in solution are completely understood, existing models for DNA-induced particle interactions are typically in error by more than an order of magnitude in strength and a factor of two in their temperature dependence. This discrepancy has stymied efforts to design the complex temperature, sequence and time-dependent interactions needed for the most interesting applications, such as materials having highly complex or multicomponent microstructures or the ability to reconfigure or self-replicate. Here we report high-spatial resolution measurements of DNA-induced interactions between pairs of polystyrene microspheres at binding strengths comparable to those used in self-assembly experiments, up to 6 k B T . We also describe a conceptually straightforward and numerically tractable model that quantitatively captures the separation dependence and temperature-dependent strength of these DNA-induced interactions, without empirical corrections. This model was equally successful when describing the more complex and practically relevant case of grafted DNA brushes with self-interactions that compete with interparticle bridge formation. Together, our findings motivate a nanomaterial design approach where unique functional structures can be found computationally and then reliably realized in experiment.colloidal iteractions | functional particles | nucleic acids | polymer entropy | optical tweezers A promising route to forming unique nanoparticle-based materials is directed self-assembly-where the interactions among multiple species of suspended particles are intentionally designed to favor the self-assembly of a specific cluster arrangement or nanostructure. DNA provides a natural tool (1-3) for directed particle assembly because DNA double helix formation is chemically specific-particles with short single-stranded DNAgrafted on their surfaces will be bridged together if and only if those strands have complementary base sequences, allowing the two strands to spontaneously hybridize to form double-stranded DNA. Moreover, the temperature-dependent stability of such DNA bridges allows the resulting attraction to be modulated (1, 2) from negligibly weak to effectively irreversible over a convenient range of temperatures. Several groups have recently used such interactions to drive the assembly of three-dimensional (3D), crystalline structures from nanoscopic (4-8) and microscopic (9, 10) particles. Ultimately, we envision a highly versatile nanomaterial design protocol in which a user-designed matrix of specific interactions among multiple particle species leads to sequential or even hierarchical assembly of complex particle structures, controlled by a user-designed thermal program. Unlike this vision of designable, sequential, and hierarchical assembly among a s...