Synthesis of crystals with a programmable kinetic barrier to nucleation

Abstract

A central goal of chemistry is to fabricate supramolecular structures of defined function and composition. In biology, control of supramolecular synthesis is often achieved through precise control over nucleation and growth processes: A seed molecule initiates growth of a structure, but this growth is kinetically inhibited in the seed's absence. Here we show how such control can be systematically designed into self-assembling structures made of DNA tiles. These structures, ''zig-zag ribbons,'' are designed to have a fixed width but can grow arbitrarily long. Under slightly supersaturated conditions, theory predicts that elongation is always favorable but that nucleation rates decrease exponentially with increasing width. We confirm experimentally that although ribbons of different widths have similar thermodynamics, nucleation rates decrease for wider ribbons. It is therefore possible to program the nucleation rate by choosing a ribbon width. The presence of a seed molecule, a stabilized version of the presumed critical nucleus, removes the kinetic barrier to nucleation of a ribbon. Thus, we demonstrate the ability to grow supramolecular structures from rationally designed seeds, while suppressing spurious nucleation. Control over DNA tile nucleation allows for proper initiation of algorithmic crystal growth, which could lead to the high-yield synthesis of micrometer-scale structures with complex programmed features. More generally, this work shows how a selfassembly subroutine can be initiated.algorithmic self-assembly ͉ DNA nanotechnology ͉ self-assembly ͉ supramolecular chemistry B iology demonstrates how self-assembly can create sophisticated organization on the molecular scale. The fundamental challenge in engineering a self-assembled object is that its molecular components must themselves contain the information needed to guide self-assembly.Controlling the nucleation of a self-assembled object is the first step in controlling the self-assembly process, as exemplified by the formation of actin networks (1, 2), the growth of microtubules on the centrosome (3), and the assembly of bacterial flagella (4). These systems avoid the difficulty of controlling homogeneous (unseeded) nucleation by relying on heterogeneous (seeded) nucleation: Growth is rare except in the presence of a seed molecule, from which it proceeds with little or no kinetic barrier. Here we demonstrate a general strategy for designing self-assembled molecular structures whose nucleation is controlled by a seed. We use programmable DNA tiles to create a series of seeded ''zig-zag ribbons'' that have increasing kinetic barriers to homogeneous nucleation.DNA tiles (5, 6) are a general-purpose nanoscale construction material. A DNA tile consists of multiple, interwoven strands that form double helices connected by ''crossover points'' (Fig. 1a). Tiles bind to each other when their single-stranded (''sticky'') ends hybridize (Fig. 1b) and can assemble into extended structures, including one-and two-dimensional crystals (7-10). Tile interactions a...

Reducing Facet Nucleation during Algorithmic Self-Assembly

“…The strands for each lattice (50 nM per strand) were annealed from 90 to 10°C over 10 h, held at 10°C for 2 h, and then melted back to 90°C at the same rate. For both lattices, we observed ( Figure 12 in Supporting Information) a reversible transition between 45 and 70°C, where tile formation has been observed previously, 3,17,24 and a hysteretic transition at lower temperatures, where lattices formed. Formation of both lattices occurred around 16°C and melted between 25 and 37°C, indicating a significant kinetic barrier to homogeneous nucleation.…”

“…We use DNA tiles ( Figure 4) to implement both uniform and snaked proofreading blocks and study their growth on long facets created using zigzag ribbons 24 (Figure 1d). See Supplementary Figures S1-S11 for sequences and diagrams of all molecules used in this work.…”

Nanoscale topographical replication of graphene architecture by artificial DNA nanostructures

“…The low thermal stability is due to the weak hydrogen bonds, with a binding energy of approximately 5 kJ/mole between DNA base pairs. 27,31,32 Fig. 2(d)-(f) show the changes in the AFM images of replicated graphene-5HRs with increasing temperature.…”

An information-bearing seed for nucleating algorithmic self-assembly

“…Finite-sized tile assemblies and self-assembled ribbon-like crystals have also been used as seeds, with improved performance ascribed to increased rigidity, but incorporating significant amounts of specific information into such seeds remains prohibitive (28,29). This motivates our interest in creating seeds that are (i) sufficiently well-formed to nucleate defect-free DNA tile crystals, (ii) capable of being synthesized with arbitrary information that the DNA tile programs can read as input, and (iii) straightforward to implement experimentally.…”