Undesired usage and the robust self-assembly of heterogeneous structures

Murugan, Arvind; Zou, James; Brenner, Michael P.

doi:10.1038/ncomms7203

Cited by 63 publications

(89 citation statements)

References 57 publications

(79 reference statements)

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“…The homogeneous model builds on previous work on virus capsid and linear protein filament assembly 15,20,[25][26][27] . The heterogeneous model in turn links to previous model systems used to study, for example, DNA-brick-based assembly of heterogeneous structures [28][29][30] . We emphasize that, even though strikingly similar experimental realizations of our model exist 11,12,31 , it is not intended to describe any particular system.…”

Section: Model Definitionmentioning

confidence: 95%

Stochastic Yield Catastrophes and Robustness in Self-Assembly

Gartner

Graf

Wilke

et al. 2019

Preprint

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A guiding principle in self-assembly is that, for high production yield, nucleation of structures must be significantly slower than their growth. However, details of the mechanism that impedes nucleation are broadly considered irrelevant. Here, we analyze self-assembly into finite-sized target structures employing mathematical modeling. We investigate two key scenarios to delay nucleation: (i) by introducing a slow activation step for the assembling constituents and, (ii) by decreasing the dimerization rate. These scenarios have widely different characteristics. While the dimerization scenario exhibits robust behavior, the activation scenario is highly sensitive to demographic fluctuations. These demographic fluctuations ultimately disfavor growth compared to nucleation and can suppress yield completely. The occurrence of this stochastic yield catastrophe does not depend on model details but is generic as soon as number fluctuations between constituents are taken into account. On a broader perspective, our results reveal that stochasticity is an important limiting factor for self-assembly and that the specific implementation of the nucleation process plays a significant role in determining the yield.

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Section: Model Definitionmentioning

confidence: 95%

Stochastic Yield Catastrophes and Robustness in Self-Assembly

Gartner

Graf

Wilke

et al. 2019

Preprint

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“…For example, in the self-assembly of a multicomponent structure, distinct but crosstalking species can take each other's place, decreasing the effective number of species. This effect has been shown to reduce selfassembly yield (27)(28)(29). Similarly, the efficacy of N parallel signaling pathways is known to be reduced by crosstalk (30).…”

Section: The Capacity Of Random Ensemblesmentioning

confidence: 99%

Information capacity of specific interactions

Huntley

Murugan

Brenner

2016

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

Self Cite

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Specific interactions are a hallmark feature of self-assembly and signal-processing systems in both synthetic and biological settings. Specificity between components may arise from a wide variety of physical and chemical mechanisms in diverse contexts, from DNA hybridization to shape-sensitive depletion interactions. Despite this diversity, all systems that rely on interaction specificity operate under the constraint that increasing the number of distinct components inevitably increases off-target binding. Here we introduce "capacity," the maximal information encodable using specific interactions, to compare specificity across diverse experimental systems and to compute how specificity changes with physical parameters. Using this framework, we find that "shape" coding of interactions has higher capacity than chemical ("color") coding because the strength of off-target binding is strongly sublinear in bindingsite size for shapes while being linear for colors. We also find that different specificity mechanisms, such as shape and color, can be combined in a synergistic manner, giving a capacity greater than the sum of the parts.S pecific interactions between many species of components are the bedrock of biochemical function, allowing signal transduction along complex parallel pathways and self-assembly of multicomponent molecular machines. Inspired by their role in biology, engineered specific interactions have opened up tremendous opportunities in materials synthesis, achieving new morphologies of self-assembled structures with varied and designed functionality. The two major design approaches for programming specific interactions use either chemical specificity or shape complementarity.Chemical specificity is achieved by dividing binding sites into smaller regions, each of which can be given one of A "colors" or unique chemical identities. Sites bind to each other based on the sum of the interactions between corresponding regions. For example, a recent two-color system paints the flat surfaces of three-dimensional polyhedra with hydrophobic and hydrophilic patterns (1) or with a pattern of solder dots (2), allowing polyhedra to stick to each other based on the registry between their surface patterns. Another popular approach uses DNA hybridization, where specific matching of complementary sequences has been used to self-assemble structures purely from DNA strands (3, 4) and from nanoparticles coated with carefully chosen DNA strands (5-9).Shape complementarity uses the shapes of the component surfaces to achieve specific binding, even though the adhesion is via a nonspecific, typically short-range potential. In the synthetic context, shape-based modulation of attractive forces over a large dynamic range was first proposed and experimentally demonstrated for colloidal particles (10, 11), using tunable depletion forces (12, 13). Recent experiments have explored the range of possibilities opened up by such ideas, from lithographically designed planar particles (14) with undulating profile patterns to "Pacman" partic...

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“…Such structures are 'addressable' in the sense that every subunit belongs in a specific location within the three-dimensional target structure [1][2][3][4][5][6] . Such structures are 'addressable' in the sense that every subunit belongs in a specific location within the three-dimensional target structure [1][2][3][4][5][6] .…”

Section: Introductionmentioning

confidence: 99%

Self-assembly protocol design for periodic multicomponent structures

Jacobs

Frenkel

2015

Soft Matter

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Assembling molecular superstructures with many distinct components will allow unprecedented control over morphology at the nanoscale. Recently, this approach has been used to assemble periodic structures with precisely defined features, such as repeating arrays of pores and channels, using a large number of building blocks. Here we propose a predictive tool that allows us to optimize the nucleation and growth of unbounded, ordered structures. In what follows, we call these structures 'crystals', even though they may only be periodic in one or two dimensions. We find that the nucleation barriers and growth pathways for crystals consisting of many components exhibit generic features that are very different from those of simple crystals. To illustrate the very non-classical nature of the nucleation and growth of such structures, we study the formation of one and two-dimensional crystals with multicomponent unit cells. We find that, whilst the boundaries in the non-periodic dimensions significantly affect the stabilities of these crystals, the nucleation barriers are largely determined by the local connectivity of the associated bulk crystal and are independent of the number of distinct components in the unit cell. We predict that the self-assembly of crystals with complex morphologies can be made to follow specific pathways toward the target structure that successively incorporate key features of the three-dimensional target structure. In contrast with simple crystals, it is possible to tune the kinetics of nucleation and growth separately, thus minimizing defect formation. We show how control over self-assembly pathways can be used to optimize the kinetics of formation of extended structures with arbitrary nanoscale patterns.

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Undesired usage and the robust self-assembly of heterogeneous structures

Cited by 63 publications

References 57 publications

Stochastic Yield Catastrophes and Robustness in Self-Assembly

Stochastic Yield Catastrophes and Robustness in Self-Assembly

Information capacity of specific interactions

Self-assembly protocol design for periodic multicomponent structures

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