Self-Assembly of a 2D DX Array

<p>Each rod represents a DNA duplex. The geometric complementarity represents the sequence complementarity of sticky ends.</p

Schematic Representation of Self-Assembly of a Sierpinski Triangle Based on XOR Operation

<p>The values in the bottom row are the inputs.</p

Basic DNA Structures for Self-Assembly

<p>(A) A four-arm junction and (B) its three-dimensional structure; (C) a DNA DX; and (D) a DNA TX.</p

A Smart DNA Tetrahedron That Isothermally Assembles or Dissociates in Response to the Solution pH Value Changes

This communication reports a DNA tetrahedron whose self-assembly is triggered by an acidic environment. The key element is the formation/dissociation of a short, cytosine (C)-containing, DNA triplex. As the solution pH value oscillates between 5.0 and 8.0, the DNA triplex will form and dissociate that, in turn, leads to assembly or disassembly of the DNA tetrahedron, which has been demonstrated by native polyacrylamide gel electrophoresis (PAGE). We believe that such environment-responsive behavior will be important for potential applications of DNA nanocages such as on-demand drug release

Solution-Phase Synthesis of DNA Amphiphiles for DNA Micellar Assembly

Hydrophobic moieties of amphiphilic DNAs can help DNAs penetrate cell membranes, but the conjugation of hydrophobic moieties to DNAs in solution phase remains challenging. Herein we report a solution-phase synthesis method to conjugate hydrophobic molecules to DNAs. This method is simple and efficient. The resulted amphiphilic DNAs can spontaneously assemble into micelles, which may serve as nanocarriers for cellular delivery of nucleic acids and water-insoluble drugs

Artificial, Parallel, Left-Handed DNA Helices

This communication reports an engineered DNA architecture. It contains multiple domains of half-turn-long, standard B-DNA duplexes. While each helical domain is right-handed and its two component strands are antiparallel, the global architecture is left-handed and the two component DNA strands are oriented parallel to each other

Fluorescence and Energy Transfer in Dye-Labeled DNA Crystals

DNA crystals make it possible to organize guest molecules into specific periodic 3D patterns at the nanoscale, and thereby to create novel macroscopic objects with potentially useful functionality. Here, we describe the fluorescence and energy transfer properties of DNA crystals that are self-assembled from DNA tensegrity triangles with covalently attached Cy3 and Cy5 dyes. When compared to reference DNA strands in solution, the fluorescence measurements indicate that the dyes in the crystal experience a more homogeneous environment, resulting in a 2-fold increase in Cy3 quantum yield and single-exponential Cy3 fluorescence decays. Energy transfer in a network of coupled Cy3 and Cy5 dyes in the DNA crystal is demonstrated experimentally. Numerical simulation finds the experiments to be consistent with a Förster model of the dyes in the periodic crystalline environment, and particularly if the transition dipoles are assumed random in orientation but static on the time scale of the excitation decay

Self-Assembly of Responsive Multilayered DNA Nanocages

Here we report the assembly of multilayered DNA nanocages. The layers can be separated in response to a chemical cue, ATP. This is an effort to increase the structural complexity of DNA nanocages. The structures have been characterized by native polyacrylamide gel electrophoresis, atomic force microscopy, and cryogenic electron microscopy. We envision that the layer-by-layer assembly strategy used in this study can be easily applied to other DNA nanocages to form Russian-doll-like semisolid structures, while the chemically activated layer separation makes a contribution to the development of “smart” DNA nanocages

Reversibly Switching the Surface Porosity of a DNA Tetrahedron

The ability to reversibly switch the surface porosity of nanocages would allow controllable matter transport in and out of the nanocages. This would be a desirable property for many technological applications, such as drug delivery. To achieve such capability, however, is challenging. Herein we report a strategy for reversibly changing the surface porosity of a self-assembled DNA nanocage (a DNA tetrahedron) that is based on DNA hydridization and strand displacement. The involved DNA nanostructures were thoroughly characterized by multiple techniques, including polyacrylamide gel electrophoresis, dynamic light scattering, atomic force microscopy, and cryogenic electron microscopy. This work may lead to the design and construction of stimuli-responsive nanocages that might find applications as smart materials

Effects of Structural Flexibility on the Kinetics of DNA Y‑Junction Assembly and Gelation

The kinetics of DNA assembly is determined not only by temperature but also by the flexibility of the DNA tiles. In this work, the flexibility effect was studied with a model system of Y-junctions, which contain single-stranded thymine (T) loops in the center. It was demonstrated that the incorporation of a loop with only one thymine prominently improved the assembly rate and tuned the final structure of the assembly, whereas the incorporation of a loop of two thymines exhibited the opposite effect. These observations could be explained by the conformation adjustment rate and the intermotif binding strength. Increasing DNA concentration hindered the conformational adjustment rate of DNA strands, leading to the formation of hydrogels in which the network was connected by ribbons. Therefore, the gel can be treated as a metastable state during the phase transition