Design strategies for self-assembly of discrete targets

Abstract

Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. Both biological and artificial self-assembly processes can take place by a range of different schemes, from the successive addition of identical building blocks to hierarchical sequences of intermediates, all the way to the fully addressable limit in which each component is unique. In this paper, we introduce an idealized model of cubic particles with patterned faces that allows self-assembly strategies to be compared and tested. We consider a simple octameric target, starting with the minimal requirements for successful self-assembly and comparing the benefits and limitations of more sophisticated hierarchical and addressable schemes. Simulations are performed using a hybrid dynamical Monte Carlo protocol that allows self-assembling clusters to rearrange internally while still providing Stokes-Einstein-like diffusion of aggregates of different sizes. Our simulations explicitly capture the thermodynamic, dynamic, and steric challenges typically faced by self-assembly processes, including competition between multiple partially completed structures. Self-assembly pathways are extracted from the simulation trajectories by a fully extendable scheme for identifying structural fragments, which are then assembled into history diagrams for successfully completed target structures. For the simple target, a one-component assembly scheme is most efficient and robust overall, but hierarchical and addressable strategies can have an advantage under some conditions if high yield is a priority. C 2015 AIP Publishing LLC.[http://dx

Effects of co-ordination number on the nucleation behaviour in many-component self-assembly

“…[4][5][6][7][8] In the past few years, several theoretical and computational studies have also been undertaken, probing the intriguing self-assembly behaviour exhibited by such systems. [9][10][11][12][13][14][15][16][17][18] We have previously shown that the DNA brick self-assembly is made possible by the interplay between self-assembly and growth. In particular, as a system of DNA bricks is cooled, at some tempera Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom.…”

Controlling Fragment Competition on Pathways to Addressable Self-Assembly

“…σ ang determines how quickly the potential decays with any deviation from perfect alignment and is set at 0.2 in this work. 16 The embedded interaction sites with angular attenuation are similar to a previous model for patchy spherical particles. [35][36][37] Each patch is also given an intrinsic orientation, pointing from the center of the face to which the patch belongs to the center of one of the face's edges.…”

“…42 However, such an approach is not advantageous in all cases. 16,43 Because of the uniqueness of building-blocks for fully addressable targets, they have no formal modularity, but a hierarchical path could nevertheless be used to limit the scope for fragment competition by controlling the fragments that are likely to arise. The performance of model A5 is shown in Fig.…”

Protein design under competition for amino acids availability

“…It became rapidly apparent that even in such simplified systems it is necessary to have a minimum number of residue types to encode the target configurations (31). Moreover, such simple models allowed to explore the related question on how the alphabet size influences protein-protein interactions (32)(33)(34)(35). Finally, works done on realistic models, offer substantial evidence that protein design with a minimalistic alphabet is possible (36)(37)(38)(39)(40).…”

“…The results show that for the folding of a small protein the minimum number of amino acid types needed is just 4. However, such a small alphabet compromises the heterogeneity of the protein-protein interactions (21,29,(33)(34)(35) and binding cannot be avoided.…”