A Signal‐Passing DNA‐Strand‐Exchange Mechanism for Active Self‐Assembly of DNA Nanostructures

Padilla, Jennifer E.; Sha, Ruojie; Kristiansen, Martin; Chen, Junghuei; Jonoska, Nataša; Seeman, Nadrian C.

doi:10.1002/ange.201500252

Cited by 9 publications

(5 citation statements)

References 33 publications

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“…The set of tiles and their sticky end sequences can control the structure of what is assembled and the pathway for assembly. Accessory DNA strands or other self-assembled complexes can also programmatically direct nucleation 26,32,33 and disassembly 34 or activate or deactivate tiles, 35 and designed DNA reaction cascades or circuits can produce outputs that in turn direct growth or assembly. 36 Increasingly precise models of assembly kinetics and structure 37 make this control reliable so that such control mechanisms can increasingly be combined to direct more complex assembly and reconfiguration processes.…”

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confidence: 99%

Terminating DNA Tile Assembly with Nanostructured Caps

et al. 2017

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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.

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confidence: 99%

Terminating DNA Tile Assembly with Nanostructured Caps

et al. 2017

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“…Recently, the group of Seeman reported a cascade reaction that is closely related to HCR but employs DNA tiles as monomer building blocks rather than hairpin loops. 580 Interestingly, the system is designed such that a binding event on one side of the tile passes a signal to the opposite side of the same tile using a switch based on toehold-mediated strand displacement. This signal "deprotects" and hence activates that side for binding to the next tile.…”

Section: Chemical Reviewsmentioning

confidence: 99%

Supramolecular Polymers in Aqueous Media

et al. 2016

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This review discusses one-dimensional supramolecular polymers that form in aqueous media. First, naturally occurring supramolecular polymers are described, in particular, amyloid fibrils, actin filaments, and microtubules. Their structural, thermodynamic, kinetic, and nanomechanical properties are highlighted, as well as their importance for the advancement of biologically inspired supramolecular polymer materials. Second, five classes of synthetic supramolecular polymers are described: systems based on (1) hydrogen-bond motifs, (2) large π-conjugated surfaces, (3) host-guest interactions, (4) peptides, and (5) DNA. We focus on recent studies that address key challenges in the field, providing mechanistic understanding, rational polymer design, important functionality, robustness, or unusual thermodynamic and kinetic properties.

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“…In this article, we demonstrate a technique for programmed self-assembly on the colloidal scale using the specific hybridization and easy design properties of DNA sequences 21 . Related schemes have been shown on molecular scales using DNA duplexes or DX motifs 22 – 24 . In our system, a family of diversely functionalized emulsion droplets… B, C, D,… are self-assembled such that C only binds to D after B binds to C. This process is controlled by using protected pairs of DNA strands on the droplets and a well-developed technology, toehold strand displacement 25 – 27 , as the enabling mechanism.…”

Section: Introductionmentioning

confidence: 99%

Sequential self-assembly of DNA functionalized droplets

et al. 2017

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Complex structures and devices, both natural and manmade, are often constructed sequentially. From crystallization to embryogenesis, a nucleus or seed is formed and built upon. Sequential assembly allows for initiation, signaling, and logical programming, which are necessary for making enclosed, hierarchical structures. Although biology relies on such schemes, they have not been available in materials science. Here, we demonstrate programmed sequential self-assembly of DNA functionalized emulsions. The droplets are initially inert because the grafted DNA strands are pre-hybridized in pairs. Active strands on initiator droplets then displace one of the paired strands and thus release its complement, which in turn activates the next droplet in the sequence, akin to living polymerization. Our strategy provides time and logic control during the self-assembly process, and offers a new perspective on the synthesis of materials.

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A Signal‐Passing DNA‐Strand‐Exchange Mechanism for Active Self‐Assembly of DNA Nanostructures

Cited by 9 publications

References 33 publications

Terminating DNA Tile Assembly with Nanostructured Caps

Terminating DNA Tile Assembly with Nanostructured Caps

Supramolecular Polymers in Aqueous Media

Sequential self-assembly of DNA functionalized droplets

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