Controlled Growth of DNA Structures From Repeating Units Using the Vernier Mechanism

Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation

Biology demonstrates how a near infinite array of complex systems and structures at many scales can originate from the self-assembly of component parts on the nanoscale. But to fully exploit the benefits of self-assembly for nanotechnology, a crucial challenge remains: How do we rationally encode well-defined global architectures in subunits that are much smaller than their assemblies? Strain accumulation via geometric frustration is one mechanism that has been used to explain the self-assembly of global architectures in diverse and complex systems a posteriori. Here we take the next step and use strain accumulation as a rational design principle to control the length distributions of self-assembling polymers. We use the DNA origami method to design and synthesize a molecular subunit known as the PolyBrick, which perturbs its shape in response to local interactions via flexible allosteric blocking domains. These perturbations accumulate at the ends of polymers during growth, until the deformation becomes incompatible with further extension. We demonstrate that the key thermodynamic factors for controlling length distributions are the intersubunit binding free energy and the fundamental strain free energy, both which can be rationally encoded in a PolyBrick subunit. While passive polymerization yields geometrical distributions, which have the highest statistical length uncertainty for a given mean, the PolyBrick yields polymers that approach Gaussian length distributions whose variance is entirely determined by the strain free energy. We also show how strain accumulation can in principle yield length distributions that become tighter with increasing subunit affinity and approach distributions with uniform polymer lengths. Finally, coarse-grained molecular dynamics and Monte Carlo simulations delineate and quantify the dominant forces influencing strain accumulation in a molecular system. This study constitutes a fundamental investigation of the use of strain accumulation as a rational design principle in molecular self-assembly.

Controlling the DNA Hybridization Chain Reaction

A novel method for controlling the oligomerization of metastable DNA hairpins using the hybridization chain reaction (HCR) is reported. Control was achieved through the introduction of a base-pair mismatch in the duplex of the hairpins. The mismatch modification allows one to kinetically differentiate initiation versus propagation events, leading to DNA oligomers up to 10 monomers long and improving dispersities from 2.5 to 1.3-1.6. Importantly, even after two consecutive chain extensions, dispersity remained unaffected, showing that well-defined block co-oligomers can be achieved. As a proof-of-concept, this technique was then applied to hairpin monomers functionalized with a mutant green fluorescent protein to prepare protein oligomers. Taken together, this work introduces an effective method for controlling living macromolecular HCR oligomerization in a manner analogous to the controlled polymerization of small molecules.

Template-Directed Synthesis of Molecular Nanorings and Cages

This Account is about templates as construction tools: molecules for making molecules. A template organizes the reactants and provides information to promote formation of a specific product, but it is not part of the final product. We have developed many different strategies for using oligopyridines as templates for the synthesis of alkyne-linked π-conjugated metalloporphyrin oligomers. These compounds include some of the largest macrocycles ever synthesized, such as a 50-porphyrin ring with a diameter of 21 nm containing a ring of 750 C-C bonds. Metalloporphyrins are excellent models for exploring template directed synthesis, as they can be functionalized in many different positions and the central metal (typically Zn or Mg) provides a handle for coordination to templates. Classical template-directed macrocyclization reactions have a 1:1 complementarity between the template and the product. This strategy works well for preparing nanorings of 5-7 porphyrin units, but larger templates are laborious to synthesize. Rings of 8 or more porphyrin units are most easily prepared using "nonclassical" strategies, in which several small templates work together to direct the formation of a large ring. In the Vernier approach, a mismatch between the number of binding sites on the template and the building block leads to a mathematical amplification of the length scale: the number of binding sites in the product is the lowest common multiple of those in the template and the building block. For example, a 40-porphyrin ring can be prepared by coupling a linear decamer in the presence of an octadentate template. Linear Vernier templating opens up intriguing possibilities for self-replication. When several small radial oligopyridine templates bind inside a large nanoring they can form complexes with some vacant coordination sites that display correlated motion like the caterpillar tracks of a bulldozer. These caterpillar track complexes can be used in template-directed synthesis and they provide the most convenient route to 8- and 10-porphyrin rings. Russian doll complexes provide another strategy for template-directed synthesis: a number of specifically designed ligands bind to a central nanoring to form a template for constructing a larger concentric nanoring. The same oligopyridine templates that are used to prepare nanorings can also be used to synthesize three-dimensional nanotubes and nanoballs. Again, nonclassical approaches, in which several small templates work together cooperatively, are much simpler than creating a single large template with sufficient binding sites to define the whole geometry of the product. Oligopyridine ligands can also be used as shadow mask templates to control the demetalation of magnesium porphyrin nanorings, because metal centers that are not coordinated by the template can be selectively demetalated with acid. Thus, the template forms a permanent shadow on the porphyrin nanostructure that remains after the template has been removed. Shadow mask templates provide a simple route to heterometalated molecular architectures. The insights emerging from these studies are widely applicable, and there are many opportunities for inventing new ways of using templates to control reactions.

Revolving Vernier Mechanism Controls Size of Linear Homomultimer

A new kind of the Vernier mechanism that is able to control the size of linear assembly of DNA origami nanostructures is proposed. The mechanism is realized by mechanical design of DNA origami, which consists of a hollow cylinder and a rotatable shaft in it connected through the same scaffold. This nanostructure stacks with each other by the shape complementarity at its top and bottom surfaces of the cylinder, while the number of stacking is limited by twisting angle of the shaft. Experiments have shown that the size distribution of multimeric assembly of the origami depends on the twisting angle of the shaft; the average lengths of the multimer are decamer, hexamer, and tetramer for 0°, 10°, and 20° twist, respectively. In summary, it is possible to affect the number of polymerization by adjusting the precise shape and movability of a molecular structure.

Template-directed synthesis of linear porphyrin oligomers: classical, Vernier and mutual Vernier

We demonstrate a variety of template-directed strategies for preparing linear monodisperse butadiyne-linked porphyrin oligomers by Glaser–Hay coupling, based on the coordination of pyridine-substituted nickel(ii) porphyrins to zinc(ii) porphyrins.

Three different types of template-directed syntheses of linear porphyrin oligomers are presented. In the classical approach the product has the same number of binding sites as the template, whereas in Vernier reactions the product has the lowest common multiple of the numbers of binding sites in the template and the building block. Mutual Vernier templating is like Vernier templating except that both strands of the Vernier complex undergo coupling simultaneously, so that it becomes impossible to say which is the ‘template’ and which is the ‘building block’. The template-directed synthesis of monodisperse linear oligomers is more difficult than that of cyclic oligomers, because the products of linear templating have reactive ends. All three types of templating are demonstrated here, and used to prepare a nickel(ii) porphyrin dodecamer with 4-pyridyl substituents on all twelve porphyrin units. The stabilities and cooperativities of the double-strand complexes involved in these reactions were investigated by UV-vis-NIR titration. The four-rung ladder duplex has a stability constant of about 2 × 10¹⁸ M^–1 in dichloromethane at 298 K.