Faisal A. Aldaye

Assembling Materials with DNA as the Guide

DNAs remarkable molecular recognition properties and structural features make it one of the most promising templates to pattern materials with nanoscale precision. The emerging field of DNA nanotechnology strips this molecule from any preconceived biological role and exploits its simple code to generate addressable nanostructures in one, two, and three dimensions. These structures have been used to precisely position proteins, nanoparticles, transition metals, and other functional components into deliberately designed patterns. They can also act as templates for the growth of nanowires, aid in the structural determination of proteins, and provide new platforms for genomics applications. The field of DNA nanotechnology is growing in a number of directions, carrying with it the promise to substantially affect materials science and biology.

Organization of Intracellular Reactions with Rationally Designed RNA Assemblies

Multidimensional RNA structures can act as scaffolds for the spatial organization of bacterial metabolism. The rules of nucleic acid base-pairing have been used to construct nanoscale architectures and organize biomolecules, but little has been done to apply this technology in vivo. We designed and assembled multidimensional RNA structures and used them as scaffolds for the spatial organization of bacterial metabolism. Engineered RNA modules were assembled into discrete, one-dimensional, and two-dimensional scaffolds with distinct protein-docking sites and used to control the spatial organization of a hydrogen-producing pathway. We increased hydrogen output as a function of scaffold architecture. Rationally designed RNA assemblies can thus be used to construct functional architectures in vivo.

Metal-nucleic acid cages.

Metal-nucleic acid cages are a promising new class of materials. Like metallo-supramolecular cages, these systems can use their metals for redox, photochemical, magnetic and catalytic control over encapsulated cargo. However, using DNA provides the potential to program pore size, geometry, chemistry and addressability, and the ability to symmetrically and asymmetrically position transition metals within the three-dimensional framework. Here we report the quantitative construction of metal-DNA cages, with the site-specific incorporation of a range of metals within a three-dimensional DNA architecture. Oligonucleotide strands containing specific environments suitable for transition-metal coordination were first organized into two DNA triangles. These triangles were then assembled into a DNA prism with linking strands. Metal centres were subsequently incorporated into the prisms at the pre-programmed locations. This unprecedented ability to position transition metals within a three-dimensional framework could lead to metal-DNA hosts with applications for the encapsulation, sensing, modification and release of biomolecules and nanomaterials.

Modular construction of DNA nanotubes of tunable geometry and single- or double-stranded character

DNA nanotubes can template the growth of nanowires, orient transmembrane proteins for nuclear magnetic resonance determination, and can potentially act as stiff interconnects, tracks for molecular motors and nanoscale drug carriers. Current methods for the construction of DNA nanotubes result in symmetrical and cylindrical assemblies that are entirely double-stranded. Here, we report a modular approach to DNA nanotube synthesis that provides access to geometrically well-defined triangular and square-shaped DNA nanotubes. We also construct the first nanotube assemblies that can exist in double- and single-stranded forms with significantly different stiffness. This approach allows for parameters such as geometry, stiffness, and single- or double-stranded character to be fine-tuned, and could enable the creation of designer nanotubes for a range of applications, including the growth of nanowires of controlled shape, the loading and release of cargo, and the real-time modulation of stiffness and persistence length within DNA interconnects.

Long-Range Assembly of DNA into Nanofibers and Highly Ordered Networks Using a Block Copolymer Approach

A simple method to introduce the long-range order achieved by block copolymers into DNA structures is described. This results in the hierarchical assembly of short DNA strands into a new one-dimensional material, with high aspect ratio and the ability to further align into highly ordered surfaces over tens of micrometers. Fibers derived from biological materials have a wide range of potential applications, such as scaffolds for nanowires and one-dimensional (1D) materials, templates for tissue growth, and ligand display tools for multivalent biological interactions. Fibers derived from short DNA strands are an attractive class of materials, as they combine long-range 1D ordering with the programmability of DNA, and its ability to undergo structure switching with specifically added DNA strands. Here, we present the first examples of long fibers self-assembled from short (10-20 base-pairs), blunt-ended DNA strands. This was accomplished by covalently attaching a dendritic oligoethylene glycol (OEG) unit to a DNA strand to form a dendritic DNA molecule (D-DNA). Hybridization of this unit with complementary DNA creates a block copolymer/double-stranded DNA architecture, which readily undergoes self-assembly into long fibers upon the addition of a selective solvent. These fibers can further align into parallel rows, to yield highly ordered micrometer-sized surfaces. We demonstrate that a DNA nanotechnology motif, a three-helix DNA bundle, can also be readily induced to form long fibers upon incorporation of D-DNA. Thus, this provides a straightforward method to introduce hierarchical long-range ordering into DNA motifs, simply through hybridization with short D-DNA strands.

A Structurally Tunable DNA-Based Extracellular Matrix

The principles of DNA nanotechnology and protein engineering have been combined to generate a new class of artificial extracellular matrices. The potential of this material for ex vivo cellular scaffolding was demonstrated using experiments in which human cervical cancer cells were found to adhere strongly, stay alive, and grow with high migration rates. The use of DNA in our DNA/protein-based matrices makes these structures inherently amenable to structural tunability. By engineering single-stranded domains into the DNA portions, we were able to fine-tune the scaffolds persistence length and stiffness as perceived by cells. This was used to direct the outcome of the cells cytoskeletal arrangement and overall shape, the status of its signal transduction protein p-FAK, and the localization of its intracellular transcription factors FOXO1a. This contribution lays the groundwork for the facile and modular construction of programmable extracellular matrices that can bring about the systematic study and replication of the naturally occurring extracellular niche.

A facile, modular and high yield method to assemble three-dimensional DNA structures.

We describe a rapid and quantitative method to generate DNA cages of deliberately designed geometry from readily available starting strands. Balancing the incorporation of sequence uniqueness and symmetry in a face-centered approach to 3D construction can result in triangular (TP), rectangular (RP), and pentagonal prisms (PP) without compromising the potential for nanostructure addressability.

Supramolecular DNA nanotechnology

Nature uses deoxyribonucleic acid (DNA) as the main material for the storage and transmission of life’s blueprint. Today, DNA is being used as a “smart” material to help solve a number of long-standing issues facing researchers in materials science and nanotechnology. In DNA nanotechnology, DNA’s powerful base-pair molecular recognition criteria are utilized to control the final structure and function of the material being generated. A sub-area of research that our group has recently termed “supramolecular DNA nanotechnology” is emerging and is extending the limits of this molecule in nanotechnology by further fine-tuning DNA’s structural and functional potential. This review will discuss the fruition and fundamentals of supramolecular DNA nanotechnology, as well as its future as a viable science in a material world.

Self-Assembly of Metal-DNA Triangles and DNA Nanotubes with Synthetic Junctions

The site-specific insertion of organic and inorganic molecules into DNA nanostructures can provide unique structural and functional capabilities. We have demonstrated the inclusion of two types of molecules. The first is a diphenylphenanthroline (dpp, 1) molecule that is site specifically inserted into DNA strands and which can be used as a template to create metal-coordinating pockets. These building blocks can then be used to assemble metal-DNA 2D and 3D structures, including metal-DNA triangles, described here. The second insertion is a triaryl molecule that provides geometric control in the preparation of 2D single-stranded DNA templates. These can be designed to further assemble into geometrically well-defined nanotubes. Here, we detail the steps involved in the construction of metal-DNA triangles and DNA nanotubes using these methods.

DNA-mediated patterning of gold nanoparticles into discrete structures: modularity, write/erase, and structural switching

Nanoparticle assemblies hold great promise as new materials in catalysis, nanoelectronic and nanophotonic applications. Many of their properties, which depend on the relative arrangement of the individual nanoparticles within the assembly, are not sufficiently well-understood because of a lack of methods to systematically assemble them into well-defined discrete model systems. In here we discuss a method for the ready access to a large number of discrete nanoparticle assemblies using a small number of single-stranded and cyclic DNA templates that are also dynamic. A triangular template and a square template are used to generate gold nanoparticle assemblies with geometrical control by the simple tagging of each particle to be organized with a DNA sequence that serves to dictate its final position within the construct. The same triangular template is used to access all the possible triangular combinations that two gold nanoparticles of different sizes may be organized in (i.e. three larger, two larger / one smaller, one larger/ two smaller, all smaller). The same square template is used to generate nanoparticle assemblies in which four gold nanoparticles are organized into square, trapezoidal and rectangular arrangements. Post-assembly addressability is demonstrated by a write/erase experiment in which three gold nanoparticles of a single size are assembled into a triangular arrangement, a specific particle is erased using an external eraser strand, and the empty position is re-written with a smaller sized particle. Our approach could be generalized to easily generate large sets of nanoparticle groupings with control over the position, size, type and addressability of each nanoparticle within the construct.