Universal two-step crystallization of DNA-functionalized nanoparticles

Dai, Wei; Kumar, Sanat K.; Starr, Francis W.

doi:10.1039/c0sm00484g

Cited by 35 publications

(36 citation statements)

References 49 publications

(107 reference statements)

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“…Another important issue to address is the rate of crystallization, since kinetic constraints play a major role in successfully generating crystal states. 32,51 Finally, since DNA-functionalized NPs have the possibility to have complex phase diagrams with multiple interpenetrating phases, 38,41,52 it will be valuable to make a similar stability analysis for more exotic interpenetrating crystal states.…”

Section: Discussionmentioning

confidence: 99%

Stability of DNA-linked nanoparticle crystals: Effect of number of strands, core size, and rigidity of strand attachment

Padovan-Merhar

Lara

Starr

2011

The Journal of Chemical Physics

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Three-dimensional ordered lattices of nanoparticles (NPs) linked by DNA have potential applications in novel devices and materials, but most experimental attempts to form crystals result in amorphous packing. Here we use a coarse-grained computational model to address three factors that impact the stability of bcc and fcc crystals formed by DNA-linked NPs : (i) the number of attached strands to the NP surface, (ii) the size of the NP core, and (iii) the rigidity of the strand attachment. We find that allowing mobility in the attachment of DNA strands to the core NP can very slightly increase or decrease melting temperature T(M). Larger changes to T(M) result from increasing the number of strands, which increases T(M), or by increasing the core NP diameter, which decreases T(M). Both results are consistent with experimental findings. Moreover, we show that the behavior of T(M) can be quantitatively described by the model introduced previously [F. Vargas Lara and F. W. Starr, Soft Matter, 7, 2085 (2011)].

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Section: Discussionmentioning

confidence: 99%

Stability of DNA-linked nanoparticle crystals: Effect of number of strands, core size, and rigidity of strand attachment

Padovan-Merhar

Lara

Starr

2011

The Journal of Chemical Physics

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“…However, there has been some progress in theory and simulation on understanding this assembly process (5, 6, 11-13). The recent work of Starr and coworkers, for example, has emphasized the complicated phase and assembly behavior of these materials (11,12,14). Travesset and coworkers (5) and Olvera de la Cruz and coworkers (15) have used large-scale molecular dynamics simulations to study equilibrium aspects and the kinetics of self-assembly, including kinetic traps like gel formation.…”

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confidence: 99%

Designing DNA-grafted particles that self-assemble into desired crystalline structures using the genetic algorithm

Srinivasan

Zhang

et al. 2013

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

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In conventional research, colloidal particles grafted with singlestranded DNA are allowed to self-assemble, and then the resulting crystal structures are determined. Although this Edisonian approach is useful for a posteriori understanding of the factors governing assembly, it does not allow one to a priori design ssDNA-grafted colloids that will assemble into desired structures. Here we address precisely this design issue, and present an experimentally validated evolutionary optimization methodology that is not only able to reproduce the original phase diagram detailing regions of known crystals, but is also able to elucidate several previously unobserved structures. Although experimental validation of these structures requires further work, our early success encourages us to propose that this genetic algorithm-based methodology is a promising and rational materials-design paradigm with broad potential applications.DNA-grafted colloids | inverse design | nanostructures | crystal lattice predictions | evolutionary algorithm A topic of much interest in the current literature is the selfassembly of colloid particles multiply grafted with ssDNA molecules (1-10). The typical experimental system consists of two types of colloids grafted with complementary ssDNA sequences. Upon cooling, hybridization of the DNA occurs, crosslinking the colloids. Under the right conditions this cross-linking can facilitate the ordering of the colloids into crystal structures. The typical dimensions of colloids result in periodicities comparable to the wavelength of visible length, which have made them attractive for various emergent technologies, e.g., photonic bandgap materials. Classes of plasmonic, light-emitting, and catalytic metamaterials can be realized via the self-assembly of ssDNAgrafted colloids into specified 3D arrays.Although much work has examined the effects of temperature, DNA length, linker DNA groups, size of colloids, etc., on structure formation, it has been largely empirically driven. However, there has been some progress in theory and simulation on understanding this assembly process (5, 6, 11-13). The recent work of Starr and coworkers, for example, has emphasized the complicated phase and assembly behavior of these materials (11,12,14). Travesset and coworkers (5) and Olvera de la Cruz and coworkers (15) have used large-scale molecular dynamics simulations to study equilibrium aspects and the kinetics of self-assembly, including kinetic traps like gel formation. Crocker and coworker developed a quantitative model based on experimental studies to predict ssDNA-induced particle interactions, the driving force for self-assembly (16). Similarly, Frenkel and coworkers has also defined a general accurate theory of valence-limited colloidal interactions (17). In a similar vein, Mirkin and coworkers proposed a rule-based complementary contact model (CCM) to predict the formation of crystal structures by ssDNA-grafted colloids (7). This model was used to explain the four crystal structures experimentally observed.Althou...

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“…Then, interpenetrating networks of DNA-functionalized NPs occur [147]. In the following study [148], a two-step crystallization of DNA-functionalized NPs has been discussed, where the narrow temperature range that the self-assembly takes place is described through a two-step process, mediated by a highly connected amorphous intermediate. Moreover, at lower temperatures, the system is kinetically trapped hindering crystallization [148].…”

Section: Coarse-grained Modelsmentioning

confidence: 99%

“…In the following study [148], a two-step crystallization of DNA-functionalized NPs has been discussed, where the narrow temperature range that the self-assembly takes place is described through a two-step process, mediated by a highly connected amorphous intermediate. Moreover, at lower temperatures, the system is kinetically trapped hindering crystallization [148]. By using a standard cluster analysis and relevant order parameters based on spherical harmonics, the structures and their degree of crystallinity were resolved.…”

Section: Coarse-grained Modelsmentioning

confidence: 99%

“…By using a standard cluster analysis and relevant order parameters based on spherical harmonics, the structures and their degree of crystallinity were resolved. The relaxation and crystallization times of such systems have been also studied [148]. Different amorphous networked phases induced by multiple liquid-liquid critical points providing a phase diagram of the temperature versus density have been identified [149], based on effective NPs.…”

Section: Coarse-grained Modelsmentioning

confidence: 99%

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Self-assembly of DNA-functionalized colloids

Theodorakis¹,

Fytas²,

Kahl³

et al. 2015

Condens. Matter Phys.

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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 remains an intensive field of research. Moreover, the fabrication of long-range structures due to kinetic bottlenecks in the self-assembly are additional challenges. Here, we discuss the most recent advances from theory and experiment with particular focus put on recent simulation studies.

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Universal two-step crystallization of DNA-functionalized nanoparticles

Cited by 35 publications

References 49 publications

Stability of DNA-linked nanoparticle crystals: Effect of number of strands, core size, and rigidity of strand attachment

Stability of DNA-linked nanoparticle crystals: Effect of number of strands, core size, and rigidity of strand attachment

Designing DNA-grafted particles that self-assemble into desired crystalline structures using the genetic algorithm

Self-assembly of DNA-functionalized colloids

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