What we work on:
Three Dimensional Cages and Nanotubes from DNA
Applications in nanopatterning and selective drug delivery to cancer cells
A major research focus in our laboratory is the construction of DNA-based architectures for applications in biology and materials science. Previous methods used only DNA to provide all design features, resulting in DNA-dense structures that are large and rigid. We developed a new approach to DNA construction, in which synthetic molecules control and modify DNA self-assembly. (Science 2008, 1795, Chem. Soc. Rev. 2011, 5647) This results in ‘DNA-economic’ structures with increased dynamic character and intrinsic functionality.
We applied this strategy to three-dimensional DNA cages and nanotubes. We showed the first modular synthesis of prismatic DNA cages with deliberate variation of size and geometry, and controlled size switching with added DNA strands. (JACS 2007, 13376, ChemComm. 2011, 8925, JACS, 2012, 4280).
We then reported a modular approach for the synthesis of DNA nanotubes, with ready control of geometry, size and stiffness of these assemblies, and ability to generate these in single-stranded ‘open’, and double-stranded ‘closed’ forms (Nature Nanotech. 2009, 349). We showed the encapsulation and selective release of cargo within our DNA cages (Nature Chem. 2010, 319, Nature Chem 2013, 868) and the control of nanotube length (J. Am. Chem. Soc. 2010, 10212, Nature Chem. 2015). These cages can be reversibly anchored on lipid bilayers (JACS 2014, 12987).
We then developed a rapid method to generate long, monodisperse DNA strands with arbitrary pre-designed sequences (1000 bases). This method will greatly simplify DNA origami and de novo protein synthesis (Nature Comm. 2015, accepted).
Some recent publications:
P. Chidchob, T. W. Edwardson, C. J. Serpell, H. F. Sleiman,
J. Am. Chem. Soc. 2016, 138 (13), pp 4416–4425.
DNA base-pairing is the central interaction in DNA assembly. However, this simple four-letter (A-T and G-C) language makes it difficult to create complex structures without using a large number of DNA strands of different sequences. Inspired by protein folding, we introduce hydrophobic interactions to expand the assembly language of DNA nanotechnology. To achieve this, DNA cages of different geometries are combined with sequence-defined polymers containing long alkyl and oligoethylene glycol repeat units. Anisotropic decoration of hydrophobic polymers on one face of the cage leads to hydrophobically-driven formation of quantized aggregates of DNA cages, where polymer length determines the cage aggregation number. Hydrophobic chains decorated on both faces of the cage can undergo an intra-scaffold ‘handshake’ to generate DNA-micelle cages, which have increased structural stability and assembly cooperativity, and can encapsulate small molecules. The polymer sequence order can control the interaction between hydrophobic blocks, leading to unprecedented ‘doughnut-shaped’ DNA cage-ring structures. We thus demonstrate that new structural and functional modes in DNA nanostructures can emerge from the synergy of two interactions, providing an attractive approach to develop protein-inspired assembly modules in DNA nanotechnology.
Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles
Thomas G. W. Edwardson, Kai Lin Lau, Danny Bousmail, Hanadi Sleiman
Nature Chemistry, Jan. 4, 2016. DOI: 10.1038/nchem.2420
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 nanotubes offer a high aspect ratio and rigidity, attractive attributes for the controlled assembly of hierarchically complex linear arrays. It is highly desirable to control the positioning of rungs along the backbone of the nanotubes, minimize the polydispersity in their manufacture and reduce the building costs. We report here a solid-phase synthesis methodology in which, through a cyclic scheme starting from a ‘foundation rung’ specifically bound to the surface, distinct rungs can be incorporated in a predetermined manner. Each rung is orthogonally addressable. Using fluorescently tagged rungs, single-molecule fluorescence studies demonstrated the robustness and structural fidelity of the constructs and confirmed the incorporation of the rungs in quantitative yield (>95%) at each step of the cycle. Prototype structures that consisted of up to 20 repeat units, about 450 nm in contour length, were constructed. Combined, the solid-phase synthesis strategy described and its visualization through single-molecule spectroscopy show good promise for the production of custom-made DNA nanotubes
Dynamic DNA Nanotubes: Reversible Switching between Single and Double-Stranded Forms, and Effect of Base Deletions
Janane Rahbani, Amani Hariri, Gonzalo Cosa* and Hanadi Sleiman*
ACS Nano 2015, 9, pp 11898–11908.
DNA nanotubes hold great potential as drug delivery vehicles and as programmable templates for the organization of materials and biomolecules. Existing methods for their construction produce assemblies that are entirely double-stranded and rigid, and thus have limited intrinsic dynamic character, or they rely on chemically modified and ligated DNA structures. Here, we report a simple and efficient synthesis of DNA nanotubes from 11 short unmodified strands, and the study of their dynamic behavior by atomic force microscopy and in situ single molecule fluorescence microscopy. This method allows the programmable introduction of DNA structural changes within the repeat units of the tubes. We generate and study fully double-stranded nanotubes, and convert them to nanotubes with one, two and three single-stranded sides, using strand displacement strategies. The nanotubes can be reversibly switched between these forms without compromising their stability and micron-scale lengths. We then site-specifically introduce DNA strands that shorten two sides of the nanotubes, while keeping the length of the third side. The nanotubes undergo bending with increased length mismatch between their sides, until the distortion is significant enough to shorten them, as measured by AFM and single-molecule fluorescence photobleaching experiments. The method presented here produces dynamic and robust nanotubes that can potentially behave as actuators, and allows their site-specific addressability while using a minimal number of component strands.
We report the anchoring of 3D-DNA-cholesterol labeled cages on spherically supported lipid bilayer membranes (SSLBM) formed on silica beads, and their addressability through strand displacement reactions, controlled membrane orientation and templated dimerization. The bilayer-anchored cages can load three different DNA-fluorophores by hybridization to their ‘top’ face (furthest from bilayer) and unload each of them selectively upon addition of a specific input displacement strand. We introduce a method to control strand displacement from their less accessible ‘bottom’ face (closest to the bilayer), by adding cholesterol-substituted displacing strands that insert into the bilayer themselves in order to access the toehold region. The orientation of DNA cages within the bilayer is tunable by positioning multiple cholesterol anchoring units on the opposing two faces of the cage, thereby controlling their accessibility to proteins and enzymes. A population of two distinct DNA cages anchored to the SSLBMs exhibited significant membrane fluidity and have been directed into dimer assemblies on bilayer via input of a complementary linking strand. Displacement experiments performed on these anchored dimers indicate that removal of only one prism’s anchoring cholesterol strand was not sufficient to release the dimers from the bilayer, however removal of both cholesterol anchors from the dimerized prisms via two displacement strands cleanly released the dimers from the bilayer. This methodology allows for the anchoring of DNA cages on supported lipid bilayers, the control of their orientation and accessibility within the bilayer, and the programmable dimerization and selective removal of any of their components. The facile coupling of DNA to other functional materials makes this an attractive method for developing stimuli-responsive protein or nanoparticle arrays, drug releasing biomedical device surfaces and self-healing materials for light harvesting applications, using a highly modular, DNA-economic scaffold.
Sequence-Responsive Unzipping DNA Cubes with Tunable Cellular Uptake Profiles
K. E. Bujold, J. Fakhoury, T. G. W. Edwardson, K. M. M. Carneiro, J. N. Briard, A. G. Godin, L. Amrein, G. D. Hamblin, L. C. Panasci, P. W. Wiseman, H. Sleiman
Chemical Science, 2014, 5, 2449-2455. Highlighted in Chemistry World (Royal Society for Chemistry), ‘DNA cube programmed for an exclusive reveal’, April 2014
Here, we demonstrate a new approach for the design and assembly of a dynamic DNA cube with an addressable cellular uptake profile. This cube can be selectively unzipped from a 3D- to a flat two-dimensional structure in the presence of a specific nucleic acid sequence. Selective opening is demonstrated in vitro using a synthetic RNA marker unique to the LNCaP human prostate cancer cell line. A robust uptake in LNCaP cells, HeLa cells (human cervical cancer) and primary B-lymphocytes isolated from the blood of chronic lymphocytic leukemia (CLL) patients is observed using fluorescence-activated cell sorting (FACS), confocal microscopy and a new cluster analysis algorithm combined with image cross-correlation spectroscopy. The DNA cube was modified with hydrophobic and hydrophilic dendritic chains that were found to coat its exterior. The dynamic, unzipping properties of these modified cubes were retained, and assessment of cellular uptake shows that the hydrophobic chains help with the rapid uptake of the constructs while the hydrophilic chains become advantageous for long term internalization.
RNA interference (RNAi) is a powerful therapeutic strategy that induces gene silencing by targeting disease-causing mRNA and can lead to their removal through degradation pathways. The potential of RNAi is especially relevant in cancer therapy, as it can be designed to regulate the expression of genes involved in all stages of tumor development (initiation, growth, and metastasis). We have generated gene silencing 3D DNA prisms that integrate antisense oligonucleotide therapeutics at 1, 2, 4, and 6 positions. Synthesis of these structures is readily achieved and leads to the assembly of highly monodisperse and well-characterized structures. We have shown antisense strands scaffolded on DNA cages can readily induce gene silencing in mammalian cells and maintain gene knockdown levels more effectively than single and double stranded controls through increased stability of bound antisense units.
T. Edwardson, C. McLaughlin, K. Carneiro, C. Serpell, H. F. Sleiman, “Dendritic Alkyl Chains on DNA Cages: A Geometry-Dependent Inter- or Intramolecular “Handshake” Nature Chem.2013, 5, 868 – 875; highlighted in McGill, Wired, Guardian, Canadian Chemical News ACCN, and a number of other media; Nature Chem. Top 10 papers in 2013 in altmetric score (http://www.nature.com/nchem/journal/v5/n10/nchem.1745/metrics)
Nature uses a combination of non-covalent interactions to create a hierarchy of complex systems from simple building blocks. One example is the selective association of hydrophobic side-chains that are a strong determinant of protein organization. Here we report a parallel mode of assembly in DNA nanotechnology. Dendritic alkyl-DNA conjugates were hybridized to the single-stranded edges of a DNA cube. When four amphiphiles are organized on a cube face, the hydrophobic residues of two neighbouring cubes engage in an intermolecular hybridization (“handshake”) resulting in a dimer. When eight amphiphiles are organized on the top and bottom faces of the cube, they engage in an intramolecular “handshake” inside the cube. This forms the first example of a monodisperse micelle within a DNA nanostructure, which encapsulates small molecules and releases them by DNA sequence recognition. Creating a three-dimensional pattern of hydrophobic patches, analogous to the array of side-chains in proteins can thus result in specific, directed association of hydrophobic domains with orthogonal interactions to DNA base-pairing.
DNA nanotubes have great potential as nanoscale scaffolds for the organization of materials, the templation of nanowires, and as drug delivery vehicles. Current methods for making DNA nanotubes either rely on a tile-based step-growth polymerization mechanism, or use a large number of component strands and long annealing times. Step-growth polymerization gives little control over length, is sensitive to stoichiometry, and is slow to generate long products. Here, we present a design strategy for DNA nanotubes that uses an alternative, more controlled growth mechanism, while using just 5 unmodified component strands and a long enzymatically produced backbone. These tubes form rapidly at room temperature, and have numerous, orthogonal sites available for the programmable incorporation of arrays of cargo along their length. As a proof-of-concept, cyanine dyes were organized into two distinct patterns by inclusion into these DNA nanotubes.
J. Conway, C. K. McLaughlin, K. Castor, H. F. Sleiman, “DNA nanostructure serum stability: greater than the sum of its parts”, Chem. Commun., 2013, 49, 1172-1174 (invited in special issue: Nucleic Acids; New Life, New Materials)
Simple chemical modifications to oligonucleotide ends with hexaethylene glycol and hexanediol are shown to significantly increase nuclease resistance under serum conditions. The modified oligonucleotides were used to construct DNA prismatic cages in a single step and in quantitative yield. These cages further stabilize their strands towards nucleases, with lifetimes of 62 hours in serum. The cages contain a large number of single-stranded regions for functionalization, illustrating their versatility for biological applications.
Sequence Controlled Polymers and DNA Nanostructures
The protein folding problem has fascinated scientists for half a century, notably in its use of multiple orthogonal interactions to create precise tertiary structure. DNA nanotechnology has reduced this complexity by using only a two base-pair code, A:T and G:C. Remarkably, we recently discovered an entirely new mode of protein-inspired interaction. We created biohybrid cages, where a 3D-DNA core structure guides the anisotropic positioning of synthetic polymer chains. (Chem. Sci, 2012, 1980, JACS 2012, 4280, Nat. Chem. 2013, 86). We developed a simple, automated method to synthesize sequence-controlled polymers attached to DNA (Angew. Chem. 2014, 4567). Combination of these precision polymers with DNA cages opens up new, unexpected assembly modes (JACS 2014, 136, 15767), with the polymer side chains either ‘shake hands’ to dimerize DNA cages (like a protein coiled coil motif), or they gather in the inside of the DNA cages to create a hydrophobic core. This cube-micelle core can encapsulate small molecule drugs, and release them selectively when specific DNA sequences are added.
Precision Polymers and 3D DNA Nanostructures: Emergent Assemblies from New Parameter Space
C. J. Serpell, T. G. W. Edwardson, P. Chidchob, K. M. M. Carneiro
J. Am. Chem. Soc. 2014, 136, 15767–15774, JACS Research Spotlight: “COMPLEX FUNCTIONALITY FROM DNA BOXES AND POLYMER SNAKES”
Polymer self-assembly and DNA nanotechnology have both proved to be powerful nanoscale techniques. To date, most attempts to merge the fields have been limited to placing linear DNA segments within a polydisperse block copolymer. Here we show that, by using hydrophobic polymers of a precisely predetermined length conjugated to DNA strands, and addressable 3D DNA prisms, we are able to effect the formation of unprecedented monodisperse quantized superstructures. The structure and properties of larger micelles-of-prisms were probed in depth, revealing their ability to participate in controlled release of their constituent nanostructures, and template light-harvesting energy transfer cascades, mediated through both the addressability of DNA and the controlled aggregation of the polymers.
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 via HPLC, dynamic light scattering, and fluorescence studies that 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.
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 via HPLC, dynamic light scattering, and fluorescence studies that 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.
A. Greschner, K. Bujold, H. F. Sleiman, “Intercalators as Molecular Chaperones in DNA Self-Assembly”, J. Am. Chem. Soc. 2013, 135, 11283–11288. Nominated by Faculty of 1000 Biology.
DNA intercalation has found many diagnostic and therapeutic applications. Here, we propose the use of simple DNA intercalators, such as ethidium bromide, as tools to facilitate the error-free self-assembly of DNA nanostructures. We show that ethidium bromide can influence DNA self-assembly, decrease the formation of oligomeric side products and cause libraries of multiple equilibrating structures to converge into a single product. Using a variety of 2D- and 3D-DNA systems, we demonstrate that intercalators present a powerful alternative for the adjustment of strand-end alignment, favor the formation of fully duplexed “closed” structures and create an environment where the smallest, most stable structure is formed. Moreover, ethidium bromide can be readily removed using isoamyl alcohol extractions combined with intercalator-specific spin columns thereby yielding the desired ready-to-use DNA structure.
K. Carneiro, N. Avakyan, H. F. Sleiman*, WIRE Nanomedicine and Nanobiotechnology: “Long-Range Assembly of DNA into Nanofibers and Organized Networks” , 2013, 5, 266-285.
Long-range assembly of DNA currently comprises both top-down and bottom-up methods. The top-down techniques consist of physical alignment of DNA and lithographic patterning to organize DNA on surfaces. The bottom-up approaches include lipid- and polymer-DNA co-assembly, the self-assembly of DNA amphiphiles, and the remarkably specific and versatile methods of DNA nanotechnology. DNA-based materials possess unprecedented molecular control and may offer innovative solutions in the fields of nanotechnology, sensing, nanomedicine as well as optical and electronic devices. To realize the potential of these materials, a number of hurdles must be addressed. Bridging the gap between top-down fabrication and bottom-up assembly is of critical importance to the successful development of functional DNA-based technology. A profound understanding of both regimes is necessary to achieve this goal.
Metal DNA Assemblies
DNA-mediated organization of multimetallic systems for applications in catalysis, artificial photosynthesis and molecular electronics
Gold Nanoparticle Assemblies
Applications in plasmonics, biosensing and nanoelectronics
Using highly functional ‘building-blocks’ of AuNPs mono-conjugated to three-dimensional DNA ‘rung’ structures, both discrete and extended linear assemblies were controllably prepared via addition of various templating backbone strands. This unique approach presents a facile alternative to other methods of AuNP organization through DNA, and has potential utility in the fields of nanophotonics and nanoelectronics.
K. L. Lau, G. Hamblin, H. Sleiman, “Gold Nanoparticle 3D-DNA Building Blocks: High Purity Preparation and Use for Modular Access to Nanoparticle Assemblies”, Small, 2013, Early View, DOI: 10.1002/smll.201301562.
Medicinal Applications of Supramolecular Complexes
Antitumor therapeutics via recognition of DNA guanine quadruplexes
A series of three platinum(II) phenanthroimidazoles each containing a protonable side-chain appended from the phenyl moiety through Copper(I)-catalyzed Azide-Alkyne Cycloaddition (CuAAC) were evaluated for their capacities to bind to human telomere, c-myc, and c-kit derived G-quadruplexes. We optimized the side-chain to enable a multivalent binding mode to G-quadruplex motifs, which would potentially result in selective targeting. Molecular modeling, high-throughput fluorescence intercalator displacement (HT-FID) assays, and surface plasmon resonance (SPR) studies demonstrate that complex 2 exhibits significantly slower dissociation rates compared to platinum phenanthroimidazoles without side-chains and other reported G-quadruplex binders. Complex 2 showed little cytotoxicity in HeLa and A172 cancer cells lines, consistent with the fact that it does not follow a telomere-targeting pathway. Preliminary mRNA analysis shows that 2 specifically interacts with the c-kit promoter region. Overall, this study validates 2 as a useful molecular probe for c-kit related cancer pathways.
K. J. Castor, Z. Liu, J. Fakhoury, M. A. Hancock, A. Mittermaier*, N. Moitessier*, H. F. Sleiman*, “A platinum(II) phenylphenanthroimidazole with an extended side-chain exhibits slow dissociation from a c-kit G-quadruplex motif”, Chem. Eur. J., 2013, 19, 17836–17845.
DNA Mimetic Polymers
Synthesis of polymers with the sequence programmability of DNA, but that are stable and readily modified through chemistry
A new class of peptide materials is introduced, integrating orthogonal aspects of peptide, nucleoside, and amphiphile chemistry. In solution, species such as rod-like or helical micelles are formed, which can lead to nanoribbons under lateral or longitudinal hierarchical growth regimes. Gelation of a wide range of solvents can be induced, including water and aqueous buffer, providing new avenues for nucleobase-specific electrophoresis, oligonucleotide delivery and bio-active cell growth media.
C. J. Serpell, M. Barłóg, K. Basu, J. F. Fakhoury, H. S. Bazzi, H. F. Sleiman, “Nucleobase Peptide Amphiphiles”, Mater. Horiz. (RSC), 2014, 1, 348-354.
Metal Containing Polymers for Diagnostic Applications
Assembly of polymer micelles containing metal centers for applications in the early diagnosis and detection of disease
The electrochemical properties and electrogenerated chemiluminescence (ECL) of an Ir(ppy)2(bpy)+-containing ROMP monomer, block copolymer (containing Ir(ppy)2(bpy)+ complexes, PEG chains, and butyl moieties), and self-assembled micelles were investigated. Following polymerization of the iridium complex, we observed multiple oxidation peaks for the block copolymer in cyclic voltammograms (CV) and differential pulse voltammograms (DPV), suggesting the presence of multiple environments for the iridium complexes along the polymer backbone. The ECL signals from monomer 1 and polymer 2 were reproducible over continuous CV cycles and stable over prolonged potential biases, demonstrating their robustness toward ECL-based detection. Comparison of the ECL signal of the block copolymer, containing multiple iridium complexes attached to the backbone, and the monomeric complex showed enhanced signals for the polymer. In fact, formation and reopening of the self-assembled micelles allowed recovery of the polymer and near complete retention of its original ECL intensity.
U. M. Tefashe, K. Metera, H. Sleiman, J. Mauzeroll, “Electrogenerated chemiluminescence of iridium-containing ROMP block copolymer and self-assembled micelles” Langmuir, 2013, 29, 12866-12873.