Entropy-Driven Crystallization Behavior in DNA-Mediated Nanoparticle Assembly

Thaner, Ryan V.; Kim, Youngeun; Li, Ting I. N. G.; Macfarlane, Robert J.; Nguyen, SonBinh T.; Cruz, Mónica Olvera de la; Mirkin, Chad A.

doi:10.1021/acs.nanolett.5b02129

Cited by 44 publications

(46 citation statements)

References 39 publications

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“…These simulations build upon previous work that has been shown to accurately predict the DNA-mediated crystallization behavior of spherical particles (23,(31)(32)(33)(34)(35); however, the broken symmetry of polyhedra requires additional considerations (SI Discussion and Tables S5-S7). Although the experimentally investigated samples are too large to model exactly, SA and D were scaled to a computationally accessible size regime in a manner consistent with experiments, and DNA density was set based on experiments (Fig.…”

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confidence: 72%

“…Calculations show that the observed transitions originate from ligand-based entropic and enthalpic contributions. In particular, an increased average inter-DNA spacing on the particle and lattice compression both indicate a wider range of less-oriented DNA states, and thus an increased free volume accessible to each DNA sticky end (32). This flexibility also allows for more DNA connections to be made between particles, as indicated by a greater F.…”

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confidence: 99%

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Exploring the zone of anisotropy and broken symmetries in DNA-mediated nanoparticle crystallization

O’Brien

Girard

Lin

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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In this work, we present a joint experimental and molecular dynamics simulations effort to understand and map the crystallization behavior of polyhedral nanoparticles assembled via the interaction of DNA surface ligands. In these systems, we systematically investigated the interplay between the effects of particle core (via the particle symmetry and particle size) and ligands (via the ligand length) on crystallization behavior. This investigation revealed rich phase diagrams, previously unobserved phase transitions in polyhedral crystallization behavior, and an unexpected symmetry breaking in the ligand distribution on a particle surface. To understand these results, we introduce the concept of a zone of anisotropy, or the portion of the phase space where the anisotropy of the particle is preserved in the crystallization behavior. Through comparison of the zone of anisotropy for each particle we develop a foundational roadmap to guide future investigations.ver the past decade, major advances in the control of nanoparticle interactions have led to powerful methods to assemble colloidal crystals (1-9). A high degree of structural control can be achieved in these methods if surface-bound ligands are used as nanoscale bonding elements to control the specificity, spacing, and strength of interactions. DNA has emerged as a particularly versatile ligand whose chemically and structurally defined nature can be used to program the symmetry, lattice parameters, and habit of colloidal crystals (1,2,7,(10)(11)(12)(13)(14)(15)(16)(17)(18)(19). The shape of the underlying nanoparticle influences the directionality of DNA interactions, which can result in correlated nanoparticle orientations and predictable crystal symmetries based on geometric considerations (7,13,16,19,20). However, predictive control can be lost if the DNA shell does not preserve the anisotropy of the particle core (13), and thus key questions pertain to (i) the phase space over which predictable directional interactions persist and (ii) the nature of the phase transitions that occur as the anisotropy of the particle disappears. Identifying this "zone of anisotropy" and the broken symmetries that form are critical to establish design rules for work with nonspherical particles and to develop nanostructured materials with controlled properties.Herein, we systematically investigate the phase space encoded by particle symmetry, particle size (L), and DNA length (D) to understand and map where directional interactions persist (Fig. 1). We show that particle symmetry dictates the crystalline states that can be accessed and how easily changes in L and D affect phase transitions between these states, which include transitions in Bravais lattice (i.e., the symmetry of how the particles are arranged within the unit cell) and particle orientation. The concepts introduced herein provide a roadmap to understand and predict particle crystallization behavior toward the construction of functional nanoparticle-based materials.To map the zone of anisotropy in DNA-mediated nan...

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confidence: 72%

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confidence: 99%

Exploring the zone of anisotropy and broken symmetries in DNA-mediated nanoparticle crystallization

O’Brien

Girard

Lin

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Stabilization of floppy crystals can be due to either enthalpy or entropy. For a single component system of DNA-coated nanoparticles [26], including the configurational entropy of the linkers in the effective potential (as adopted in this work), the b.c.c. crystal is believed to be favored over the f.c.c.…”

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Entropy Stabilizes Floppy Crystals of Mobile DNA-Coated Colloids

Ruiz

2018

Phys. Rev. Lett.

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Grafting linkers with open ends of complementary single-stranded DNA makes a flexible tool to tune interactions between colloids, which facilitates the design of complex self-assembly structures. Recently, it has been proposed to coat colloids with mobile DNA linkers, which alleviates kinetic barriers without high-density grafting, and also allows the design of valency without patches. However, the self-assembly mechanism of this novel system is poorly understood. Using a combination of theory and simulation, we obtain phase diagrams for the system in both two and three dimensional spaces, and find stable floppy square and CsCl crystals when the binding strength is strong, even in the infinite binding strength limit. We demonstrate that these floppy phases are stabilized by vibrational entropy, and "floppy" modes play an important role in stabilizing the floppy phases for the infinite binding strength limit. This special entropic effect in the self-assembly of mobile DNA-coated colloids is very different from conventional molecular self-assembly, and it offers new axis to help design novel functional materials using mobile DNA-coated colloids.Nucleic acids are ubiquitous in nature because of their capability of encoding large amounts of information via canonical Watson-Crick base-paring interactions [1]. With the help of chemical methods to make synthetic oligonucleotides of arbitrary sequences, one can use specific binding interactions between single-stranded DNA (ssDNA) chains to program selective interactions between different colloidal particles. For example, one can graft DNA linkers to the surface of colloidal particles with open ends of ssDNAs. These ssDNA tails serve as "sticky ends" that bind specifically to other colloids coated with ssDNA tails of complementary sequence, which offers a novel way of manipulating the self-assembly of colloidal particles [2,3]. By using DNA-coated colloids (DNACCs), a number of ordered crystals [4-10] and selfassembled "colloidal molecules" [11] have been obtained in experiments, while the self-assembly mechanism of DNACCs is still not well understood [9,12,13]. For example, the diffusionless transformation from a floppy crystal to the other compact crystal has been observed in experimental systems while the underlying mechanism remains not fully resolved [13].Recently, a novel system of mobile DNA-coated colloids (mDNACCs) was introduced that displays qualitatively new properties [14,15]. Compared with immobile DNA-coated colloidal systems, mDNACCs have a broader temperature window for self-assembly, and therefore allow the better control over the assembly process [14]. Mobility of DNA linkers also allows particles to more easily roll around each other and rearrange [14,16], without grafting of very high density. Moreover, unlike colloids with patches in specific locations [11,16], the interaction in mDNACCs is intrinsically a many-body potential, which could be employed to control the "valency" of particles without patches by tuning nonspecific repulsions between the p...

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“…Bond strength can even be postsynthetically increased through the use of ruthenium coordination complexes, ethidium bromide, or silver ion intercalators . While dsDNA is relatively stiff, the flexibility of DNA strands between PAEs can be independently tuned by incorporating ssDNA bases or polyethylene glycol “flexors” to affect crystallization ability and quality or alter the entropic penalty associated with PAE bond formation, which can result in alterations to PAE superlattice structure …”

Section: Versatility In the Pae Constructmentioning

confidence: 99%

“…While the predominant driving force that dictated the thermodynamically favorable lattice structure for a given set of PAEs was initially discovered to be almost entirely an enthalpic maximization of DNA binding, it was later found that entropic effects could be increased with flexible DNA linkers, thereby inducing self‐complementary PAEs to form a bcc lattice even though this structure represents a lower packing density than the prior fcc structures that had been obtained in unary systems . Making the core–core interactions appreciable in scale, one study created the binary phase isostructural to sodium‐thallium (NaTl) .…”

Section: Versatility In the Pae Constructmentioning

confidence: 99%

Programmable Atom Equivalents: Atomic Crystallization as a Framework for Synthesizing Nanoparticle Superlattices

Gabrys

Zornberg

Macfarlane

2019

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Decades of research efforts into atomic crystallization phenomenon have led to a comprehensive understanding of the pathways through which atoms form different crystal structures. With the onset of nanotechnology, methods that use colloidal nanoparticles (NPs) as nanoscale “artificial atoms” to generate hierarchically ordered materials are being developed as an alternative strategy for materials synthesis. However, the assembly mechanisms of NP‐based crystals are not always as well‐understood as their atomic counterparts. The creation of a tunable nanoscale synthon whose assembly can be explained using the context of extensively examined atomic crystallization will therefore provide significant advancement in nanomaterials synthesis. DNA‐grafted NPs have emerged as a strong candidate for such a “programmable atom equivalent” (PAE), because the predictable nature of DNA base‐pairing allows for complex yet easily controlled assembly. This Review highlights the characteristics of these PAEs that enable controlled assembly behaviors analogous to atomic phenomena, which allows for rational material design well beyond what can be achieved with other crystallization techniques.

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Entropy-Driven Crystallization Behavior in DNA-Mediated Nanoparticle Assembly

Cited by 44 publications

References 39 publications

Exploring the zone of anisotropy and broken symmetries in DNA-mediated nanoparticle crystallization

Exploring the zone of anisotropy and broken symmetries in DNA-mediated nanoparticle crystallization

Entropy Stabilizes Floppy Crystals of Mobile DNA-Coated Colloids

Programmable Atom Equivalents: Atomic Crystallization as a Framework for Synthesizing Nanoparticle Superlattices

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