skip to main content

Attention:

The NSF Public Access Repository (PAR) system and access will be unavailable from 11:00 PM ET on Thursday, February 13 until 2:00 AM ET on Friday, February 14 due to maintenance. We apologize for the inconvenience.


Title: Surface-assisted self-assembly of 2D, DNA binary crystals
Surface-assisted, tile-based DNA self-assembly is a powerful method to construct large, two-dimensional (2D) nanoarrays. To further increase the structural complexity, one idea is to incorporate different types of tiles into one assembly system. However, different tiles have different adsorption strengths to the solid surface. The differential adsorptions make it difficult to control the effective molar ratio between different DNA tile concentrations on the solid surface, leading to assembly failure. Herein, we propose a solution to this problem by engineering the tiles with comparable molecular weights while maintaining their architectures. As a demonstration, we have applied this strategy to successfully assemble binary DNA 2D arrays out of very different tiles. We expect that this strategy would facilitate assembly of other complicated nanostructures as well.  more » « less
Award ID(s):
2025187 2107393
PAR ID:
10441731
Author(s) / Creator(s):
; ; ; ; ;
Publisher / Repository:
Royal Society of Chemistry
Date Published:
Journal Name:
Nanoscale
Volume:
15
Issue:
23
ISSN:
2040-3364
Page Range / eLocation ID:
9941 to 9945
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Assembly of complex structures from a small set of tiles is a common theme in biology. For example, many copies of identical proteins make up polyhedron-shaped, viral capsids and tubulin can make long microtubules. This inspired the development of tile-based DNA self-assembly for nanoconstruction, particularly for structures with high symmetries. In the final structure, each type of motif will adopt the same conformation, either rigid or with defined flexibility. For structures that have no symmetry, their assembly remains a challenge from a small set of tiles. To meet this challenge, algorithmic self-assembly has been explored driven by computational science, but it is not clear how to implement this approach to one-dimensional (1D) structures. Here, we have demonstrated that a constant shift of a conformational equilibrium could allow 1D structures to evolve. As shown by atomic force microscopy imaging, one type of DNA tile successfully assembled into DNA spirals and concentric circles, which became less and less curved from the structure's center outward. This work points to a new direction for tile-based DNA assembly. 
    more » « less
  2. Abstract

    Tile‐based DNA self‐assembly is a powerful approach for nano‐constructions. In this approach, individual DNA single strands first assemble into well‐defined structural tiles, which, then, further associate with each other into final nanostructures. It is a general assumption that the lower‐level structures (tiles) determine the higher‐level, final structures. In this study, we present concrete experimental data to show that higher‐level structures could, at least in the current example, also impact on the formation of lower‐level structures. This study prompts questions such as: how general is this phenomenon in programmed DNA self‐assembly and can we turn it into a useful tool for fine tuning DNA self‐assembly?

     
    more » « less
  3. Abstract

    Motivated by applications in DNA-nanotechnology, theoretical investigations in algorithmic tile-assembly have blossomed into a mature theory. In addition to computational universality, the abstract Tile Assembly Model (aTAM) was shown to be intrinsically universal (FOCS 2012), a strong notion of completeness where a single tile set is capable of simulating the full dynamics of all systems within the model; however, this construction fundamentally required non-deterministic tile attachments. This was confirmed necessary when it was shown that the class of directed aTAM systems, those where all possible sequences of tile attachments result in the same terminal assembly, is not intrinsically universal (FOCS 2016). Furthermore, it was shown that the non-cooperative aTAM, where tiles only need to match on 1 side to bind rather than 2 or more, is not intrinsically universal (SODA 2014) nor computationally universal (STOC 2017). Building on these results to further investigate the other dynamics, Hader et al. examined several tile-assembly models which varied across (1) the numbers of dimensions used, (2) how tiles diffused through space, and (3) whether each system is directed, and determined which models exhibited intrinsic universality (SODA 2020). In this paper we extend those results to provide direct comparisons of the various models against each other by considering intrinsic simulations between models. Our results show that in some cases, one model is strictly more powerful than another, and in others, pairs of models have mutually exclusive capabilities. This paper is a greatly expanded version of that which appeared in ICALP 2023.

     
    more » « less
  4. Topologically Interlocked Material systems are a class of architectured materials. TIM systems are assembled from individual building blocks and are confined by an external frame. In particular, 2D, plate-type assemblies are considered. This publication contains files for the numerical analysis of the mechanical behavior of TIM systems through the use of finite element analysis. ABAQUS model files (inp format) for the study of the chiral/achiral response are provided. Files chirality_s1_in.inp are for type I square assemblies. n=3,5,7,9 Files chirality_s2_in.inp are for type II square assemblies. n=4,6,8,10 Files chirality_h1_in.inp are for type I hexagon assemblies. n=2,3,4,5 Files chirality_h2_in.inp are for type II hexagon assemblies. n=2,3,4,5 File chirality_s1i5_center_dissection.inp is for an assembly with a dissection of the central tile of type I square assembly with n=5. File chirality_s2i6_center_dissection.inp is for an assembly with a dissection of the central tile of type II square assembly with n=6. File chirality_s1i5_center_surrounding_dissection.inp is for an assembly with dissections of the tiles surrounding the center tile of type I square assembly with n=5. File chirality_h1i3_center_dissection.inp is for an assembly with a dissection of the central tile of type I hexagon assembly with n=3. File chirality_h2i3_center_dissection.inp is for an assembly with a dissection of the central tile of type II hexagon assembly with n=3. File chirality_h1i3_center_surrounding_dissection.inp is for an assembly with dissections of the tiles surrounding the center tile of type I hexagon assembly with n=3. 
    more » « less
  5. Inspired by nature and motivated by a lack of top-down tools for precise nanoscale manufacture, self-assembly is a bottom-up process where simple, unorganized components autonomously combine to form larger more complex structures. Such systems hide rich algorithmic properties - notably, Turing universality - and a self-assembly system can be seen as both the object to be manufactured as well as the machine controlling the manufacturing process. Thus, a benchmark problem in self-assembly is the unique assembly of shapes: to design a set of simple agents which, based on aggregation rules and random movement, self-assemble into a particular shape and nothing else. We use a popular model of self-assembly, the 2-handed or hierarchical tile assembly model, and allow the existence of repulsive forces, which is a well-studied variant. The technique utilizes a finely-tuned temperature (the minimum required affinity required for aggregation of separate complexes). We show that calibrating the temperature and the strength of the aggregation between the tiles, one can encode the shape to be assembled without increasing the number of distinct tile types. Precisely, we show one tile set for which the following holds: for any finite connected shape S, there exists a setting of binding strengths between tiles and a temperature under which the system uniquely assembles S at some scale factor. Our tile system only uses one repulsive glue type and the system is growth-only (it produces no unstable assemblies). The best previous unique shape assembly results in tile assembly models use O(K(S)/(log K(S))) distinct tile types, where K(S) is the Kolmogorov (descriptional) complexity of the shape S. 
    more » « less