Mobile Linkers on DNA-Coated Colloids: Valency without Patches

Angioletti‐Uberti, Stefano; Varilly, Patrick; Mognetti, Bortolo Matteo; Frenkel, Daan

doi:10.1103/physrevlett.113.128303

Cited by 86 publications

(146 citation statements)

References 31 publications

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“…Controlled valence of isotropic mesoscale particles has been demonstrated (18,32). The interaction among monomers needs to strengthen in time, so that they do not aggregate in solution, but do bind to each other during time they are attached to the template.…”

Section: Discussionmentioning

confidence: 99%

Spontaneous emergence of catalytic cycles with colloidal spheres

Zeravcic

Brenner

2017

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

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Colloidal particles endowed with specific time-dependent interactions are a promising route for realizing artificial materials that have the properties of living ones. Previous work has demonstrated how this system can give rise to self-replication. Here, we introduce the process of colloidal catalysis, in which clusters of particles catalyze the creation of other clusters through templating reactions. Surprisingly, we find that simple templating rules generically lead to the production of huge numbers of clusters. The templating reactions among this sea of clusters give rise to an exponentially growing catalytic cycle, a specific realization of Dyson's notion of an exponentially growing metabolism. We demonstrate this behavior with a fixed set of interactions between particles chosen to allow a catalysis of a specific sixparticle cluster from a specific seven-particle cluster, yet giving rise to the catalytic production of a sea of clusters of sizes between 2 and 11 particles. The fact that an exponentially growing cycle emerges naturally from such a simple scheme demonstrates that the emergence of exponentially growing metabolisms could be simpler than previously imagined.catalytic cycles | DNA-coated colloids | metabolism | templating T he origin of life is usually associated with self-replication, the ability of an entity to create copies of itself (1). Thus inspired, there have been many efforts in recent years aimed at creating artificial systems with self-replicative capacity. These are typically inspired by the linear chain mechanism of DNA. However, living systems are more than individual entities that can replicate themselves. Dyson (2) and Oparin (3) argued that a more critical aspect of living systems is the creation of a metabolism, a complex cascade of chemical reactions that together are able to accomplish more than any single chemical reaction can do on its own. Using a simple mathematical model, the so-called "garbage bag model," Dyson presented a scenario through which such a complex metabolism could arise spontaneously. His idea is that a random set of catalysts will catalyze arbitrary chemical reactions in a nonsynergistic fashion. However, if each catalyst is more likely to function when there are others that are synergistic with it, then there is a critical amount of cooperativity above which metabolic cycles spontaneously emerge. This idea has been explored through abstract simulations (4). In a similar spirit, Kauffman and coworkers have shown that if the probability of one species catalyzing the formation of another is above a threshold, then catalytic cycles naturally emerge (5-7).Whether this scenario can naturally occur in practice remains obscure. The fundamental question is to determine how likely it is for a soup of interacting catalysts to self-organize into an exponentially growing catalytic cycle. How special do the interactions between the different components need to be for spontaneous exponentially growing catalytic cycles to emerge? In this work, we present an explicit demon...

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Section: Discussionmentioning

confidence: 99%

Spontaneous emergence of catalytic cycles with colloidal spheres

Zeravcic

Brenner

2017

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

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“…Linkers on particles B i can form inter-particle bridges b i , with particles A. In the following, we consider linkers constituted by double stranded DNA spacers of length L = 10 nm and point-like sticky ends, 21 rigid particles of radius R = 10 L, 21 and N = 100. See Sec.…”

Section: Binding Cooperativity In Dna-functionalized Particlesmentioning

confidence: 99%

“…Our results are exact in the limit of many linkers per particle. 21,22 We envisage applications of our theory to the association of more complex molecules like DNA tiles [23][24][25] or virial caspids. 26 In Sec.…”

Section: Introductionmentioning

confidence: 99%

Communication: Free energy of ligand-receptor systems forming multimeric complexes

Michele

Bachmann

Parolini

et al. 2016

The Journal of Chemical Physics

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Ligand-receptor interactions are ubiquitous in biology and have become popular in materials in view of their applications to programmable self-assembly. Although complex functionalities often emerge from the simultaneous interaction of more than just two linker molecules, state of the art theoretical frameworks enable the calculation of the free energy only in systems featuring one-to-one ligand/receptor binding. In this Communication, we derive a general formula to calculate the free energy of systems featuring simultaneous direct interaction between an arbitrary number of linkers. To exemplify the potential and generality of our approach, we apply it to the systems recently introduced by Parolini et al. [ACS Nano 10, 2392

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“…Looked from another perspective, this can be rationalised as a weaker effective ligand-receptor bond strength, due to the entropic penalty of localising the pair inside the patch area. 53 Surface functionalisation of nanoparticles is used not only to graft targeting ligands, but also to protect their surface. For example, dense brushes of poly-ethylene-glycol (PEG), a highly bio-inert polymer, are often used to prevent the adsorption of serum protein and to reduce the non-specific uptake of nanoparticles by macrophages.…”

Section: Predicting and Controlling Nanoparticles Endocytosismentioning

confidence: 99%

Theory, simulations and the design of functionalized nanoparticles for biomedical applications: A Soft Matter Perspective

Angioletti‐Uberti

2017

npj Comput Mater

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Functionalised nanoparticles for biomedical applications represents an incredibly exciting and rapidly growing field of research. Considering the complexity of the nano-bio interface, an important question is to what extent can theory and simulations be used to study these systems in a realistic, meaningful way. In this review, we will argue for a positive answer to this question. Approaching the issue from a "Soft Matter" perspective, we will consider those properties of functionalised nanoparticles that can be captured within a classical description. We will thus not concentrate on optical and electronic properties, but rather on the way nanoparticles' interactions with the biological environment can be tuned by functionalising their surface and exploited in different contexts relevant to applications. In particular, we wish to provide a critical overview of theoretical and computational coarsegrained models, developed to describe these interactions and present to the readers some of the latest results in this fascinating area of research.

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Mobile Linkers on DNA-Coated Colloids: Valency without Patches

Cited by 86 publications

References 31 publications

Spontaneous emergence of catalytic cycles with colloidal spheres

Spontaneous emergence of catalytic cycles with colloidal spheres

Communication: Free energy of ligand-receptor systems forming multimeric complexes

Theory, simulations and the design of functionalized nanoparticles for biomedical applications: A Soft Matter Perspective

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