Chengde Mao

Logical computation using algorithmic self-assembly of DNA triple-crossover molecules

Recent work has demonstrated the self-assembly of designed periodic two-dimensional arrays composed of DNA tiles, in which the intermolecular contacts are directed by ‘sticky’ ends. In a mathematical context, aperiodic mosaics may be formed by the self-assembly of ‘Wang’ tiles, a process that emulates the operation of a Turing machine. Macroscopic self-assembly has been used to perform computations; there is also a logical equivalence between DNA sticky ends and Wang tile edges. This suggests that the self-assembly of DNA-based tiles could be used to perform DNA-based computation. Algorithmic aperiodic self-assembly requires greater fidelity than periodic self-assembly, because correct tiles must compete with partially correct tiles. Here we report a one-dimensional algorithmic self-assembly of DNA triple-crossover molecules that can be used to execute four steps of a logical (cumulative XOR) operation on a string of binary bits.

A nanomechanical device based on the B - Z transition of DNA

The assembly of synthetic, controllable molecular mechanical systems is one of the goals of nanotechnology. Protein-based molecular machines, often driven by an energy source such as ATP, are abundant in biology,. It has been shown previously that branched motifs of DNA can provide components for the assembly of nanoscale objects, links and arrays. Here we show that such structures can also provide the basis for dynamic assemblies: switchable molecular machines. We have constructed a supramolecular device consisting of two rigid DNA ‘double-crossover’ (DX) molecules connected by 4.5 double-helical turns. One domain of each DX molecule is attached to the connecting helix. To effect switchable motion in this assembly, we use the transition between the B and Z, forms of DNA. In conditions that favour B-DNA, the two unconnected domains of the DX molecules lie on the same side of the central helix. In Z-DNA-promoting conditions, however, these domains switch to opposite sides of the helix. This relative repositioning is detected by means of fluorescence resonance energy transfer spectroscopy, which measures the relative proximity of two dye molecules attached to the free ends of the DX molecules. The switching event induces atomic displacements of 20–60 Å.

From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal

We live in a macroscopic three-dimensional (3D) world, but our best description of the structure of matter is at the atomic and molecular scale. Understanding the relationship between the two scales requires a bridge from the molecular world to the macroscopic world. Connecting these two domains with atomic precision is a central goal of the natural sciences, but it requires high spatial control of the 3D structure of matter. The simplest practical route to producing precisely designed 3D macroscopic objects is to form a crystalline arrangement by self-assembly, because such a periodic array has only conceptually simple requirements: a motif that has a robust 3D structure, dominant affinity interactions between parts of the motif when it self-associates, and predictable structures for these affinity interactions. Fulfilling these three criteria to produce a 3D periodic system is not easy, but should readily be achieved with well-structured branched DNA motifs tailed by sticky ends. Complementary sticky ends associate with each other preferentially and assume the well-known B-DNA structure when they do so; the helically repeating nature of DNA facilitates the construction of a periodic array. It is essential that the directions of propagation associated with the sticky ends do not share the same plane, but extend to form a 3D arrangement of matter. Here we report the crystal structure at 4 Å resolution of a designed, self-assembled, 3D crystal based on the DNA tensegrity triangle. The data demonstrate clearly that it is possible to design and self-assemble a well-ordered macromolecular 3D crystalline lattice with precise control.

Conformational flexibility facilitates self-assembly of complex DNA nanostructures

Molecular self-assembly is a promising approach to the preparation of nanostructures. DNA, in particular, shows great potential to be a superb molecular system. Synthetic DNA molecules have been programmed to assemble into a wide range of nanostructures. It is generally believed that rigidities of DNA nanomotifs (tiles) are essential for programmable self-assembly of well defined nanostructures. Recently, we have shown that adequate conformational flexibility could be exploited for assembling 3D objects, including tetrahedra, dodecahedra, and buckyballs, out of DNA three-point star motifs. In the current study, we have integrated tensegrity principle into this concept to assemble well defined, complex nanostructures in both 2D and 3D. A symmetric five-point-star motif (tile) has been designed to assemble into icosahedra or large nanocages depending on the concentration and flexibility of the DNA tiles. In both cases, the DNA tiles exhibit significant flexibilities and undergo substantial conformational changes, either symmetrically bending out of the plane or asymmetrically bending in the plane. In contrast to the complicated natures of the assembled structures, the approach presented here is simple and only requires three different component DNA strands. These results demonstrate that conformational flexibility could be explored to generate complex DNA nanostructures. The basic concept might be further extended to other biomacromolecular systems, such as RNA and proteins.

Bottom-up Assembly of RNA Arrays and Superstructures as Potential Parts in Nanotechnology

DNA and protein have been extensively scrutinized for feasibility as parts in nanotechnology, but another natural building block, RNA, has been largely ignored. RNA can be manipulated to form versatile shapes, thus providing an element of adaptability to DNA nanotechnology, which is predominantly based upon a double-helical structure. The DNA-packaging motor of bacterial virus phi29 contains six DNA-packaging RNAs (pRNA), which together form a hexameric ring via loop/loop interaction. Here we report that this pRNA can be redesigned to form a variety of structures and shapes, including twins, tetramers, rods, triangles, and 3D arrays several microns in size via interaction of programmed helical regions and loops. Three dimensional RNA array formation required a defined nucleotide number for twisting of the interactive helix and a palindromic sequence. Such arrays are unusually stable and resistant to a wide range of temperatures, salt concentrations, and pH.

Complex wireframe DNA origami nanostructures with multi-arm junction vertices

Structural DNA nanotechnology and the DNA origami technique, in particular, have provided a range of spatially addressable two- and three-dimensional nanostructures. These structures are, however, typically formed of tightly packed parallel helices. The development of wireframe structures should allow the creation of novel designs with unique functionalities, but engineering complex wireframe architectures with arbitrarily designed connections between selected vertices in three-dimensional space remains a challenge. Here, we report a design strategy for fabricating finite-size wireframe DNA nanostructures with high complexity and programmability. In our approach, the vertices are represented by n × 4 multi-arm junctions (n = 2-10) with controlled angles, and the lines are represented by antiparallel DNA crossover tiles of variable lengths. Scaffold strands are used to integrate the vertices and lines into fully assembled structures displaying intricate architectures. To demonstrate the versatility of the technique, a series of two-dimensional designs including quasi-crystalline patterns and curvilinear arrays or variable curvatures, and three-dimensional designs including a complex snub cube and a reconfigurable Archimedean solid were constructed.

Cascade signal amplification for DNA detection

This paper reports a novel, isothermal DNA-detection method that integrates two steps of signal amplification: one by a protein enzyme and the other by a DNA enzyme (DNAzyme). Each analyte DNA molecule triggers a polymerase-mediated rollingcircle amplification (RCA) to produce a linear array of DNA peroxidases that catalyze a chemical oxidation and generate a colorimetric output. The current detection limit is 1 pm. DNA detection plays a critical role in biomedical research and clinical diagnostics. Extensive efforts have developed many sensitive methods based on modern biotechnology and nanotechnology, including the use of DNAzymes. DNAzymes can catalyze chemical reactions and amplify output signals. More importantly, they are more stable and robust than protein enzymes. Such properties lead to the wide use of DNAzymes in DNA detection. For instance, RNA-cleaving DNAzymes together with molecular beacons have been used in DNA detection, reaching a detection limit of 10 pm. Recently, Willner and co-workers have explored a method based on a preidentified DNA peroxidase that is a G-quadruplex–hemin complex. This DNAzyme catalyzes chemical reactions that generate chemiluminescence or produce colored products. If a DNA analyte molecule can only activate one DNAzyme, the detection will not be very sensitive. One way to overcome this problem is to introduce Au nanoparticles (AuNPs) as biobarACHTUNGTRENNUNGcodes. AuNPs are functionalized with many copies of DNAzymes. When an AuNP is immobilized to a solid surface by a DNA target molecule, multiple copies of DNAzymes will be immobilized and generate a strong output signal. DNAzymes can also be very efficiently produced by PCR, a thermal cycling technique. Based on the DNA peroxidase, we have developed an efficient way to amplify isothermal signals that greatly improves the detection limit. Our strategy contains two successive steps of isothermal, enzymatic amplification (Figure 1).

Surface-Mediated DNA Self-Assembly

This communication reports a strategy for solid surface-mediated DNA self-assembly. DNA molecules weakly interact with solid surfaces; thus are confined to solid surfaces. The confinement reduces the flexibility of DNA nanomotifs and promotes the DNA 2D crystals to grow on solid surfaces. As a demonstration, periodic DNA nanoarrays have been directly assembled onto mica surfaces. Such in situ assembly eliminates the sample transfer process between assembly and characterization and possible applications.

DNA Nanotubes as Combinatorial Vehicles for Cellular Delivery

This work explores using self-assembled DNA nanostructures as carriers for drug delivery. We have recently developed an organic nanotube system that is assembled from a single component: a 52-base-long DNA single strand. In this work, functional agents (folate as a cancer cell target agent and Cy3 as a fluorescence imaging agent) are conjugated with the DNA strands; the conjugates self-assemble into micrometers-long nanotubes (NTs). The conjugated DNA-NTs can be effectively taken by cancer cells as demonstrated by fluorescence imaging and fluorescence-activated cell sorting. No obvious toxicity has been observed under current experimental conditions.

Symmetry Controls the Face Geometry of DNA Polyhedra

Two complementary strategies have been developed to control the face geometry during the self-assembly of DNA polyhedra from branched DNA nanomotifs (tiles). In these approaches, any two interacting tiles are not equivalent in terms of either sequence or orientation; thus, each face must contain an even number of tiles. As a demonstration, DNA cubes, whose each face contains four tiles, have been assembled through these approaches.