Synchronization of Two Assembly Processes To Build Responsive DNA Nanostructures

Herein, we report a strategy for the synchronization of two self‐assembly processes to assemble stimulus‐responsive DNA nanostructures under isothermal conditions. We hypothesized that two independent assembly processes, when brought into proximity in space, could be synchronized and would exhibit positive synergy. To demonstrate this strategy, we assembled a ladderlike DNA nanostructure and a ringlike DNA nanostructure through two hybridization chain reactions (HCRs) and an HCR in combination with T‐junction cohesion, respectively. Such proximity‐induced synchronization adds a new element to the tool box of DNA nanotechnology. We believe that it will be a useful approach for the assembly of complex and responsive nanostructures.     

Programmed‐Assembly System Using DNA Jigsaw Pieces

A novel method for assembling multiple DNA origami structures has been developed by using designed 2D DNA origami rectangles, so‐called “DNA jigsaw pieces” that have sequence‐programmed connectors. Shape and sequence complementarity were introduced to the concavity and convex connectors in the DNA rectangles for selective connection with the help of nonselective π‐stacking interactions between the side edges of the DNA jigsaw piece structures. Single DNA jigsaw piece units were assembled into unidirectional nanostructures with the correct alignment and uniform orientation. Three and five different DNA jigsaw pieces were assembled into predesigned and ordered nanostructures in a programmed fashion. Finally, three‐, four‐, and five‐letter words have been displayed by using this programmed DNA jigsaw piece system.     

Directed Self‐Assembly of DNA Tiles into Complex Nanocages

Tile‐based self‐assembly is a powerful method in DNA nanotechnology and has produced a wide range of well‐defined nanostructures. But the resulting structures are relatively simple. Increasing the structural complexity and the scope of the accessible structures is an outstanding challenge in molecular self‐assembly. A strategy to partially address this problem by introducing flexibility into assembling DNA tiles and employing directing agents to control the self‐assembly process is presented. To demonstrate this strategy, a range of DNA nanocages have been rationally designed and constructed. Many of them can not be assembled otherwise. All of the resulting structures have been thoroughly characterized by gel electrophoresis and cryogenic electron microscopy. This strategy greatly expands the scope of accessible DNA nanostructures and would facilitate technological applications such as nanoguest encapsulation, drug delivery, and nanoparticle organization.     

DNA‐Grafted Supramolecular Polymers: Helical Ribbon Structures Formed by Self‐Assembly of Pyrene–DNA Chimeric Oligomers

The controlled arraying of DNA strands on adaptive polymeric platforms remains a challenge. Here, the noncovalent synthesis of DNA‐grafted supramolecular polymers from short chimeric oligomers is presented. The oligomers are composed of an oligopyrenotide strand attached to the 5′‐end of an oligodeoxynucleotide. The supramolecular polymerization of these oligomers in an aqueous medium leads to the formation of one‐dimensional (1D) helical ribbon structures. Atomic force and transmission electron microscopy show rod‐like polymers of several hundred nanometers in length. DNA‐grafted polymers of the type described herein will serve as models for the development of structurally and functionally diverse supramolecular platforms with applications in materials science and diagnostics.     

Surface‐Assisted Large‐Scale Ordering of DNA Origami Tiles

The arrangement of DNA‐based nanostructures into extended higher order assemblies is an important step towards their utilization as functional molecular materials. We herein demonstrate that by electrostatically controlling the adhesion and mobility of DNA origami structures on mica surfaces by the simple addition of monovalent cations, large ordered 2D arrays of origami tiles can be generated. The lattices can be formed either by close‐packing of symmetric, non‐interacting DNA origami structures, or by utilizing blunt‐end stacking interactions between the origami units. The resulting crystalline lattices can be readily utilized as templates for the ordered arrangement of proteins.     

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

DNA nanostructured tiles play an active role in their own self‐assembly in the system described herein whereby they initiate a binding event that produces a cascading assembly process. We present DNA tiles that have a simple but powerful property: they respond to a binding event at one end of the tile by passing a signal across the tile to activate a binding site at the other end. This action allows sequential, virtually irreversible self‐assembly of tiles and enables local communication during the self‐assembly process. This localized signal‐passing mechanism provides a new element of control for autonomous self‐assembly of DNA nanostructures.     

A Case Study of the Likes and Dislikes of DNA and RNA in Self‐Assembly

Programmed self‐assembly of nucleic acids (DNA and RNA) is an active research area as it promises a general approach for nanoconstruction. Whereas DNA self‐assembly has been extensively studied, RNA self‐assembly lags much behind. One strategy to boost RNA self‐assembly is to adapt the methods of DNA self‐assembly for RNA self‐assembly because of the chemical and structural similarities of DNA and RNA. However, these two types of molecules are still significantly different. To enable the rational design of RNA self‐assembly, a thorough examination of their likes and dislikes in programmed self‐assembly is needed. The current work begins to address this task. It was found that similar, two‐stranded motifs of RNA and DNA lead to similar, but clearly different nanostructures.     

Soft-surface DNA nanotechnology: DNA constructs anchored and aligned to lipid membrane

No strings attached: At least three attachment points are needed to align a two-dimensional DNA nanoconstruct to a soft lipid membrane surface with a porphyrin nucleoside as membrane anchor. The resulting freely diffusing DNA constructs can be reversibly assembled on the surface thus enabling the possibility of a self-repairing system.     

Structural Transformation: Assembly of an Otherwise Inaccessible DNA Nanocage

A strategy of structural transformation for the assembly of DNA nanocages that can not be assembled directly is described. In this strategy, a precursor DNA nanocage is assembled first and then is isothermally transformed into a desired, complicated nanocage. A dramatic, conformational change accompanies the transformation. This strategy has been proven to be successful by native polyacrylamide gel electrophoresis (PAGE) and cryogenic electron microscopy (cryoEM) imaging. We expect that the strategy of structural transformation will be useful for the assembly of many otherwise inaccessible DNA nanostructures and help to increase the structural complexity of DNA nanocages.