Risheng Wang

Crystalline Two‐Dimensional DNA‐Origami Arrays

Nanotechnology aims to organize matter with the highest possible accuracy and control. Such control will lead to nanoelectronics, nanorobotics, programmable chemical synthesis, scaffolded crystals, and nanoscale systems responsive to their environments. Structural DNA nanotechnology1 is one of the most powerful routes to this goal. It combines robust branched DNA species with the control of affinity and structure2 inherent in the programmability of sticky ends. The successes of structural DNA nanotechnology include the formation of objects,3 2D crystals,4 3D crystals,5 nanomechanical devices,6 and various combinations of these species (e.g., ref. 7). DNA origami8 is arguably the most effective way of producing a large addressable area on a 2D DNA surface. This method entails the combination of a long single strand (typically M13 single-stranded form, 7249 nucleotides) with about ~250 staple strands to define its shape and patterning. With a pixilation estimated at about 6 nm,8 it is possible to build patterns with about 100 addressable points within a definable shape in an area of about 10,000 nm2. Many investigators have sought unsuccessfully to increase the useful size of 2D origami units by forming crystals of individual origami tiles.0 Here, we report the 2D crystallization of origami tiles to yield a 2D array with dimensions 2–3 microns on an edge. This size is likely to be large enough to connect bottom-up methods of patterning with top-down approaches.

Assembly of Heterogeneous Functional Nanomaterials on DNA Origami Scaffolds

One on each side: gold nanoparticles (AuNPs) and semiconducting quantum dots (QDs) are integrated on a single DNA origami scaffold. Streptavidin-functionalized QDs bind to biotin anchors on one side of the DNA origami, while DNA-coated AuNPs bind through DNA hybridization to single-stranded DNA on the other side of the scaffold. This approach offers a new path toward the organization of complex systems consisting of disparate materials.

Prototyping Nanorod Control: A DNA Double Helix Sheathed within a DNA Six-Helix Bundle

The control of the structure of matter is a key goal of nanoscience. DNA is an exciting molecule for control because it forms programmable intermolecular interactions. Stiff DNA structures, such as the double crossover motif, the tensegrity triangle, and the six-helix bundle (6HB) have been used to produce periodic arrays of DNA components. The 6HB motif consists of six DNA double helices flanking an inner cavity whose diameter is similar to that of a double helix. This motif appears to be an excellent candidate to sheathe and control nanorods by inserting them into the cavity, and then to control the placement and orientation of the rod by controlling the DNA sheath. Here, we prototype this kind of control by using a seventh DNA double helix as the nanorod and fixing it inside the 6HB motif.

Blunt-ended DNA stacking interactions in a 3-helix motif

We demonstrate that intermolecular stacking is capable of forming one-dimensional arrays of a blunt-ended 3-helix DNA motif. The array can be visualized in the atomic force microscopy through conjugated streptavidin nanoparticles. We estimate the strength of the triple stacking interaction to be -8.6 kcal mol(-1).

Selective placement of DNA origami on substrates patterned by nanoimprint lithography

Self-assembled DNA nanostructures can be used as scaffolds to organize small functional nanocomponents. In order to build working devices—electronic circuits, biochips, optical/photonics devices—controlled placement of DNA nanostructures on substrates must be achieved. Here we present a nanoimprint lithography-based process to create chemically patterned templates, rendering them capable of selectively binding DNA origami. Hexamethyldisilazane (HMDS) is used as a passivating layer on silicon dioxide substrates, which prevents DNA attachment. Hydrophilic areas, patterned by nanoimprint lithography with the same size and shape of the origami, are formed by selective removal of the HMDS, enabling the assembly of the origami scaffolds in the patterned areas. The use of nanoimprint lithography, a low cost, high throughput patterning technique, enables high precision positioning and orientation of DNA nanostructures on a surface over large areas.

Directed Assembly of End-Functionalized Single Wall Carbon Nanotube Segments

A key impediment to the implementation of a nanoelectronics technology based on single wall carbon nanotubes (SWCNTs) is the inability to arrange them in a manner suitable for integration into complex circuits. As a step toward addressing this problem, we explore the binding of fixed-length, end-functionalized SWCNT segments to lithographically defined nanoscale anchors, such that individual SWCNTs can be placed with control over position and orientation. Both monovalent and bivalent bindings are explored using covalent and noncovalent binding chemistries. Placement efficiency is assessed in terms of overall yield of SWCNT binding, as well as binding specificity and the degree of nonspecific binding. Placement yields as high as 93% and 79% are achieved, respectively, for covalent binding and for binding through DNA hybridization. Orientational control of the SWCNT segments is achieved with 95% and 51% efficiency for monovalent and bivalent bindings, respectively. This represents a new approach that could pave the way toward complex SWCNT devices and circuits.

Thermodynamic Analysis of Nylon Nucleic Acids

The stability and structure of nylon nucleic acid duplexes with complementary DNA and RNA strands was examined. Thermal denaturing studies of a series of oligonucleotides that contained nylon nucleic acids (1–5 amide linkages) revealed that the amide linkage significantly enhanced the binding affinity of nylon nucleic acids towards both complementary DNA (up to 26 °C increase in the thermal transition temperature (Tm) for five linkages) and RNA (around 15 °C increase in Tm for five linkages) compared with nonamide linked precursor strands. For both DNA and RNA complements, increasing derivatization decreased the melting temperatures of uncoupled molecules relative to unmodified strands; by contrast, increasing lengths of coupled copolymer raised Tm from less to slightly greater than Tm of unmodified strands. Thermodynamic data extracted from melting curves and CD spectra of nylon nucleic acid duplexes were consistent with loss of stability due to incorporation of pendent groups on the 2′‐position of ribose and recovery of stability upon linkage of the side chains.

Lithographically directed assembly of one-dimensional DNA nanostructures via bivalent binding interactions

AbstractIn order to exploit the outstanding physical properties of one-dimensional (1D) nanostructures such as carbon nanotubes and semiconducting nanowires and nanorods in future technological applications, it will be necessary to organize them on surfaces with precise control over both position and orientation. Here, we use a 1D rigid DNA motif as a model for studying directed assembly at the molecular scale to lithographically patterned nanodot anchors. By matching the inter-nanodot spacing to the length of the DNA nanostructure, we are able to achieve nearly 100% placement yield. By varying the length of single-stranded DNA linkers bound covalently to the nanodots, we are able to study the binding selectivity as a function of the strength of the binding interactions. We analyze the binding in terms of a thermodynamic model which provides insight into the bivalent nature of the binding, a scheme that has general applicability for the controlled assembly of a broad range of functional nanostructures.