Hanadi F. Sleiman

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.

Rolling Circle Amplification-Templated DNA Nanotubes Show Increased Stability and Cell Penetration Ability

DNA nanotubes hold promise as scaffolds for protein organization, as templates of nanowires and photonic systems, and as drug delivery vehicles. We present a new DNA-economic strategy for the construction of DNA nanotubes with a backbone produced by rolling circle amplification (RCA), which results in increased stability and templated length. These nanotubes are more resistant to nuclease degradation, capable of entering human cervical cancer (HeLa) cells with significantly increased uptake over double-stranded DNA, and are amenable to encapsulation and release behavior. As such, they represent a potentially unique platform for the development of cell probes, drug delivery, and imaging tools.

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.

Nucleobase-templated polymerization: copying the chain length and polydispersity of living polymers into conjugated polymers.

Conjugated polymers synthesized by step polymerization mechanisms typically suffer from poor molecular weight control and broad molecular weight distributions. We report a new method which uses nucleobase recognition to read out and efficiently copy the controlled chain length and narrow molecular weight distribution of a polymer template generated by living polymerization, into a daughter conjugated polymer. Aligning nucleobase-containing monomers on their complementary parent template using hydrogen-bonding interactions, and subsequently carrying out a Sonogashira polymerization, leads to the templated synthesis of a conjugated polymer. Remarkably, this daughter strand is found to possess a narrow molecular weight distribution and a chain length nearly equivalent to that of the parent template. On the other hand, nontemplated polymerization or polymerization with the incorrect template generates a short conjugated oligomer with a significantly broader molecular weight distribution. Hence, nucleobase-templated polymerization is a useful tool in polymer synthesis, in this case allowing the use of a large number of polymers generated by living methods, such as anionic polymerization, controlled radical polymerizations (NMP, ATRP, and RAFT) and other mechanisms to program the structure, length, and molecular weight distribution of polymers normally generated by step polymerization methods and significantly enhance their properties.

Self-assembly of three-dimensional DNA nanostructures and potential biological applications.

A current challenge in nanoscience is to achieve controlled organization in three-dimensions, to provide tools for biophysics, molecular sensors, enzymatic cascades, drug delivery, tissue engineering, and device fabrication. DNA displays some of the most predictable and programmable interactions of any molecule, natural or synthetic. As a result, 3D-DNA nanostructures have emerged as promising tools for biology and materials science. In this review, strategies for 3D-DNA assembly are discussed. DNA cages, nanotubes, dendritic networks, and crystals are formed, with deliberate variation of their size, shape, persistence length, and porosities. They can exhibit dynamic character, allowing their selective switching with external stimuli. They can encapsulate and position materials into arbitrarily designed patterns, and show promise for numerous biological and materials applications.

Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles

DNA nanotechnology offers unparalleled precision and programmability for the bottom-up organization of materials. This approach relies on pre-assembling a DNA scaffold, typically containing hundreds of different strands, and using it to position functional components. A particularly attractive strategy is to employ DNA nanostructures not as permanent scaffolds, but as transient, reusable templates to transfer essential information to other materials. To our knowledge, this approach, akin to top-down lithography, has not been examined. Here we report a molecular printing strategy that chemically transfers a discrete pattern of DNA strands from a three-dimensional DNA structure to a gold nanoparticle. We show that the particles inherit the DNA sequence configuration encoded in the parent template with high fidelity. This provides control over the number of DNA strands and their relative placement, directionality and sequence asymmetry. Importantly, the nanoparticles produced exhibit the site-specific addressability of DNA nanostructures, and are promising components for energy, information and biomedical applications. DNA nanostructures are typically used as molecular scaffolds. Now, it has been shown that they can also act as reusable templates for ‘molecular printing’ of DNA strands onto gold nanoparticles. The products inherit the recognition elements of the parent template: number, orientation and sequence asymmetry of DNA strands. This converts isotropic nanoparticles into complex building blocks.

An Efficient and Modular Route to Sequence‐Defined Polymers Appended to DNA

Inspired by biological polymers, sequence-controlled synthetic polymers are highly promising materials that integrate the robustness of synthetic systems with the information-derived activity of biological counterparts. Polymer-biopolymer conjugates are often targeted to achieve this union; however, their synthesis remains challenging. We report a stepwise solid-phase approach for the generation of completely monodisperse and sequence-defined DNA-polymer conjugates using readily available reagents. These polymeric modifications to DNA display self-assembly and encapsulation behavior-as evidenced by HPLC, dynamic light scattering, and fluorescence studies-which is highly dependent on sequence order. The method is general and has the potential to make DNA-polymer conjugates and sequence-defined polymers widely available.

Three-dimensional organization of block copolymers on "DNA-minimal" scaffolds.

Here, we introduce a 3D-DNA construction method that assembles a minimum number of DNA strands in quantitative yield, to give a scaffold with a large number of single-stranded arms. This DNA frame is used as a core structure to organize other functional materials in 3D as the shell. We use the ring-opening metathesis polymerization (ROMP) to generate block copolymers that are covalently attached to DNA strands. Site-specific hybridization of these DNA-polymer chains on the single-stranded arms of the 3D-DNA scaffold gives efficient access to DNA-block copolymer cages. These biohybrid cages possess polymer chains that are programmably positioned in three dimensions on a DNA core and display increased nuclease resistance as compared to unfunctionalized DNA cages.

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.