Terminating DNA Tile Assembly with Nanostructured Caps

Abstract

Precise control over the nucleation, growth, and termination of self-assembly processes is a fundamental tool for controlling product yield and assembly dynamics. Mechanisms for altering these processes programmatically could allow the use of simple components to self-assemble complex final products or to design processes allowing for dynamic assembly or reconfiguration. Here we use DNA tile self-assembly to develop general design principles for building complexes that can bind to a growing biomolecular assembly and terminate its growth by systematically characterizing how different DNA origami nanostructures interact with the growing ends of DNA tile nanotubes. We find that nanostructures that present binding interfaces for all of the binding sites on a growing facet can bind selectively to growing ends and stop growth when these interfaces are presented on either a rigid or floppy scaffold. In contrast, nucleation of nanotubes requires the presentation of binding sites in an arrangement that matches the shape of the structure's facet. As a result, it is possible to build nanostructures that can terminate the growth of existing nanotubes but cannot nucleate a new structure. The resulting design principles for constructing structures that direct nucleation and termination of the growth of one-dimensional nanostructures can also serve as a starting point for programmatically directing two- and three-dimensional crystallization processes using nanostructure design.

Feedback regulation of crystal growth by buffering monomer concentration

“…For example, if the growth load is eliminated, monomers should not accumulate to push the reaction into the unseeded regime as would be expected for open loop regulation. To test whether monomer buffering could compensate for the complete elimination of load, we added DNA origami caps, which attach to nanotube ends, preventing further growth, in excess of seeds after different growth times 38 (Fig. 6d).…”

“…To demonstrate how monomer buffering can regulate crystallization, we grow DNA nanotubes from oligomeric DNA monomers 8,38 while buffering the nanotube monomer concentration. DNA nanotube growth is a well-understood model system for studying crystallization 8,23,39,40 .…”

Active Self‐Assembly of Train‐Shaped DNA Nanostructures via Catalytic Hairpin Assembly Reactions

“…[19] Schulman and co-workers used nano structured caps to terminate DNA tile assembly. [20] Lau and Sleiman reported the assembly of 1D DNA tile structures using sequentially grown input strands as a template. [21] Despite these successes, the synthesis of well-defined finite DNA nanostructures with dynamic characteristics remains an important challenge.…”

“…Seeman and co‐workers presented a signal‐passing DNA‐strand‐exchange mechanism for the active self‐assembly of DNA nanowires . Schulman and co‐workers used nanostructured caps to terminate DNA tile assembly . Lau and Sleiman reported the assembly of 1D DNA tile structures using sequentially grown input strands as a template .…”

Biomimetische DNA‐Nanoröhren: Gezielte Synthese und Anwendung nanoskopischer Kanäle

“…Die Forscher beendeten den Assemblierungsvorgang durch Zugabe von Nano‐Deckeln aus DNA. Die durchschnittliche Länge der Nanoröhren war hierbei zeitabhängig . Aus diesen Designs entwickelten sich Punkt‐zu‐Punkt zusammengefügte Nanoröhren, um je zwei Zielstrukturen in unterschiedlicher Entfernungen und Orientierung zu verbinden (Abbildung ).…”