Research

Highlights:

Loading and Selective Release of Cargo in DNA Nanotubes with Longitudinal Variation

Peggy Lo, Pierre Karam, Faisal Aldaye, Graham Hamblin, Gonzalo Cosa, Hanadi Sleiman

Nature Chemistry 2010,2, 319-328 (LINK)

Selected for Faculty of 1000 Biology (LINK), Research highlights in Chemistry World (Royal Society for Chemistry, “All Aboard the DNA Nanotube, LINK), Nano Today (Elsevier, LINK), Quebec Science (June 2010 , "L'ADN en Lego" (LINK)) , and in popular media : Interview with Rutherford radio show, Alberta (March 19, 2010), Asharq Awsat newspaper (link 1, link 2) and various web science media (see McGill release, LINK)

Nanotubes hold promise for a number of biological and materials applications, owing to their high aspect ratio and encapsulation potential.  A particularly attractive goal is to access nanotubes that exert well-defined control over their cargo, such as selective encapsulation, precise positioning of the guests along the nanotube length, and triggered release of this cargo in response to specific external stimuli.    We here report the construction of DNA nanotubes with longitudinal variation, and an alternation of larger and smaller capsules along the tube length.  Size-selective encapsulation of gold nanoparticles into the large capsules of these tubes leads to ‘nanopeapod’ particle lines with positioning of the particles 65 nm apart.  These nanotubes can then be opened with specific added DNA strands, with spontaneous release of their particle cargo.  This approach can lead to new applications of self-assembled nanotubes, such as in precise 1D-nanomaterials organization, gene-triggered selective delivery of drugs, and biological sensing. 

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

Karina M. M. Carneiro, Faisal A. Aldaye and Hanadi F. Sleiman

J. Am. Chem. Soc. 2009, 132, 679-685

Selected as Editor's Choice in Science Magazine, Feb 12, 2010 issue, 'Materials Science: Stringing DNA Alone' (LINK)

This manuscript describes the hierarchical assembly of short DNA strands into a new one-dimensional material, with long-range ordering, high aspect ratio, stiffness, and the ability to further align into highly ordered surfaces over tens of microns. DNA has recently emerged as a highly promising template for the programmable and precise positioning of materials on the nanometer scale.  However, long-range assembly has been a challenge in DNA nanotechnology, because it requires the incorporation of a large number of distinct DNA sequences, and results in significant errors in the extended structures.  On the other hand, synthetic block copolymers have been extensively investigated for their ability to achieve long-range ordering through microphase separation of dissimilar blocks.  However, block copolymers are not intrinsically programmable in the same manner as DNA.
This contribution describes a combination of these two materials, DNA for its programmability and a block copolymer architecture for its ability to confer long-range ordering on the final structure.  Specifically, we report the synthesis of a DNA molecule (D-DNA) composed of a short DNA strand (10-20 bases) covalently attached to a dendritic oligoethylene glycol (OEG) moiety.  By hybridizing D-DNA with a complementary strand, a DNA triblock copolymer is formed.  Upon addition of an organic solvent, these molecules self-assemble into very stiff fibers, that are a few nanometers in diameter but microns in length.  These are composed of a DNA core protected from the organic solvent by the OEG dendrons.  These further align into highly organized DNA surfaces composed of parallel, braided fibers.  Thus, the present contribution provides an exceedingly simple method to introduce hierarchical long-range ordering of DNA motifs, simply by hybridization with short D-DNA strands.
One-dimensional biological materials have been extensively investigated towards a number of potential biological and materials applications. The extended 1D-structures in this contribution can potentially lend their use in fields ranging from gene delivery vehicles, programmable and addressable scaffolds for tissue growth, dynamic materials for nanopatterning in 1D and 2D, and templates for nanowire fabrication.

Templated Ligand Environments for the Selective Incorporation of Different Metals into DNA

Hua Yang, Andrzej Z. Rys, Christopher K. McLaughlin, and Hanadi F. Sleiman

Angew. Chem. 2009, 48, 9919-9923. (LINK)

Selected for the front cover of Angewandte Chemie

This contribution describes the site-specific introduction of different transition metals within a DNA environment.  The incorporation of metals into DNA allows the transfer of functionality, such as enhanced stability, redox, photo-activity, magnetic and catalytic properties, to this otherwise passive molecule.  It results in expanding the DNA ‘alphabet’ into new metal ‘letters’, which can increase the information content of this biomolecule and reduce errors in its assembly to nanostructures.  However, the selective incorporation of metals into DNA has been challenging, because many metals non-specifically bind and can even cleave this biomolecule.
In this contribution, we describe the DNA-templated  creation of different ligand environments that are selective for their binding metals: (terpyridine)2 selective for iron(II), (diphenylphenanthroline)2 selective for copper(I) and mixed (terpyridine)(diphenylphenanthroline), selective for copper(II).  Dramatic stabilization by these transition metals was conferred onto the DNA duplex, with FeII resulting in one of the highest reported melting temperature increases for any single modification to a DNA strand.  Moreover, when the ‘incorrect’ metal ion is placed within one of these metal environments, ‘error correction’ occurs: the metal can spontaneously adjust its redox state, displace another labile metal to form a more-stable complex, or reorganize the coordination site to create a more favored complex.
Thus, in a similar manner to the ligand pockets of metalloenzymes, this new class of DNA-templated coordination environments defines a toolbox for site-specifically incorporating different transition metals into DNA.  It provides the opportunity to use DNA’s programmable character to position different metals into deliberately designed patterns, which is currently a difficult goal to achieve using conventional supramolecular chemistry.  This programmable positioning of metals can lead to applications of these assemblies in artificial photosynthesis, multimetallic catalysis, magnetic materials, nanoelectronics and nanophotonics.

Metal-Nucleic Acid Cages

Hua Yang, Christopher McLaughlin, Graham Hamblin, Faisal Aldaye, Andrzej Rys, H. F. Sleiman
(H. Yang and C. McLaughlin contributed equally to this manuscript)

Nature Chemistry, 2009, 1, 390 (LINK)

News and Views coverage in Nature Chemistry (LINK)

Metal-nucleic acid cages are a promising new class of materials.  Like their metallo-supramolecular cage counterparts, these systems could use their metals to provide redox, photochemical, magnetic, and catalytic control over their encapsulated cargo.  However, the use of DNA provides the potential to readily program pore size, geometry, chemistry and addressability, and the unprecedented ability to symmetrically and asymmetrically position different transition metals within the 3D framework.  We here report the quantitative construction of the first metal 3D DNA cages, with site-specific incorporation of a range of metals.  The approach involves the use of 2D DNA triangular intermediates containing ligand vertices, their assembly into 3D DNA prisms, and their subsequent use to programmably organize specific metal centers.  Overall, this opens the door to the facile construction of tailor-made, functional metal-DNA host structures, with potential applications as stimuli-responsive frameworks for the encapsulation, sensing, modification and release of biomolecules and nanomaterials.

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

F. A. Aldaye, P. K. Lo, P. Karam, C. K. McLaughlin, G. Cosa & H. F. Sleiman

Nature Nanotechnology, 2009, doi:10.1038/nnano.2009.72 (LINK)

News Coverage (LINK)

DNA nanotubes can template the growth of nanowires, orient transmembrane proteins for NMR 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 provide access to 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

P. K. Lo, H. F. Sleiman

J. Am. Chem. Soc., 2009, 131, 4182-4183 (LINK)

Editor’s Choice in Nature Chemistry (“Conjugated Polymers: Template Trickery”), March 2009 (LINK)

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, non-templated polymerization, or polymerization with the incorrect template generates a short conjugated oligomer with 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.

F. A. Aldaye, A. Palmer, H. F. Sleiman

Science, invited review, 2008, 321, 1795.

DNA’s 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 significantly impact materials science and biology.

Templated Synthesis of Highly Stable, Electroactive and Dynamic Metal-DNA Branched Junctions

H. Yang, H. F. Sleiman

Angew. Chem., 2008, 47, 2443-2446

Selected to appear as the cover page of the journal.

This work describes a new template method, which allows the incorporation of kinetically labile transition metals into DNA junctions.  This creates remarkably stable and electroactive metal-DNA branch points, in which the metal complexes are in intimate contact with the DNA stack.  In addition, this approach gives access to the first reported dynamic multimetallic DNA nanostructures, with metal centers at their vertices, single stranded DNA as their sides, and DNA double strands at their periphery.  We demonstrate quantitative and reversible structural switching of these metal-DNA nanostructures by adding specific DNA strands, resulting in controlled modulation of the metal-metal distances. Overall, this study enables the use of a large number of metal centers to directly affect the function of DNA nanostructures, through their redox, luminescence, magnetic and catalytic properties, as well as the structure of DNA assemblies, through the plethora of geometries and coordination environments available to them. 

A Platinum Supramolecular Square as an Effective G-Quadruplex Binder and Telomerase Inhibitor

R. Kieltyka, P. Englebienne, J. Fakhoury, C. Autexier, N. Moitessier, H. Sleiman

J. Am.Chem. Soc., 2008, 130, 10040-10041

In this contribution, we report that a self-assembled platinum molecular square [Pt(en)(4,4’-dipyridyl)]4 can act as an efficient G-quadruplex binder and telomerase inhibitor. Molecular modeling studies show that the square arrangement of the four bipyridyl ligands, the highly electropositive nature of the overall complex, as well as hydrogen bonding interactions between the ethylenediamine ligands and phosphates of the DNA backbone all contribute to the observed strong binding affinity to the G-quadruplex. Through thermal denaturation studies with duplex and quadruplex FRET probes, CD studies and enzymatic assays, we demonstrate that this platinum square strongly binds to G-quadruplexes, and can act as an inhibitor of telomerase. This study thus shows the potential of supramolecular self-assembly to readily generate scaffolds of unique geometries for effective targeting of G-quadruplexes, and for the ultimate development of selective antitumor therapies.

Modular Generation of Structurally Switchable 3D- DNA Assemblies

J. Am. Chem. Soc., 2007, 13376-13377

Highlighted in the journals Nature (“Gene Boxes”), Nature Materials (“Unnatural Life”) and ACS NANO (“Inspiration from Biology”)

Faisal Aldaye, Hanadi F. Sleiman

This contribution describes a new method that allows ready access to a large number of three-dimensional DNA assemblies, and demonstrates, for the first time, their structural switching in response to external stimuli.  3D-construction is a current challenge in DNA nanotechnology.  DNA polyhedra present tremendous potential in a number of areas, including drug encapsulation and release, regulation of the folding and activity of encaged proteins, as host molecules for nanomaterials and as building blocks for 3D-networks for catalysis and biomolecule crystallization.  However, 3D-DNA assemblies have typicallly been difficult to access.  Moreover, no reports have described structurally dynamic or stimuli responsive systems, which is a requirement for the potential of such DNA objects for encapsulation and selective release to be realized.  This manuscript describes the pre-assembly of single stranded and cyclic DNA triangles, squares, pentagons and hexagons with rigid organic vertices, and their use as building blocks for modular access to a large number of three-dimensional objects.  A triangular prism, a cube, pentameric and hexameric prisms, as well as more complex structures such as a heteroprism and biprism were readily and quantitatively accessed through the modular combination of these primary building blocks.  In principle, any structure that can be retrosynthetically broken down to such DNA cycles can be readily accessed using this approach, and as such, this represents a highly economical method to build diversity in three-dimensional DNA assembly.  In addition, we show the addressability of these assemblies, by constructing a dynamic triangular prism capable of real-time structural oscillation between three predefined lengths, and demonstrating the dynamic transformation of this capsule by fluorescence energy transfer (FRET) studies.  A number of applications can be anticipated for these switchable capsules, including molecule-triggered drug delivery, modulation of the properties of encaged molecules or materials with cavity size, and dynamic three-dimensional DNA crystals.

Guest-Mediated Access to a Single DNA Nanostructure from a Library of Multiple Assemblies

J. Am. Chem. Soc. 2007, 129, 10070-10071

Faisal Aldaye, Hanadi F. Sleiman

This contribution describes the first use of a small molecule guest to control the outcome and significantly increase selectivity in DNA self-assembly.  There has been increased interest in the use of DNA as a component in nanoscience.  However, as the complexity of DNA nanosystems increases, so will the number of different DNA sequences that need to be incorporated.  This inevitably leads to the inclusion of degenerate sequences which can assemble into undesirable secondary structures.  The process of error control and correction is currently a real bottleneck towards the creation of more complex DNA systems.  In this manuscript, we show that the addition of a small molecule can template the formation of a single DNA nanostructure, from building blocks which otherwise assemble into a large number of possible structures.  We then use this simple method to template the formation of well-defined, one-dimensional DNA fibers which are nanometers in diameter and tens of microns in length, from trifunctional building blocks that would form ill-defined networks without the template.  Considering the wealth of DNA-binding molecules that can be used to refine, correct and modify DNA self-assembly, this approach promises to lead to significant advances in the area of DNA nanotechnology.

Platinum Phenanthroimidazole Complexes as G-Quadruplex DNA Selective Binders

Chem. Eur. J. 2008, 14, 1145-1154

Roxanne Kieltyka, Johans Fakhoury, Nicolas Moitessier and Hanadi F. Sleiman

Stuck on G-quadruplexes:  Complexes that bind and stabilize G-quadruplex DNA structures are of significant interest due to their potential to inhibit telomerase and halt cancer cell proliferation.  A series of pi-extended phenanthroimidazole PtII complexes were synthesized.  Their relative binding affinities to duplex and quadruplex DNA were studied through UV-vis, CD and competitive equilibrium dialysis.  Significant binding affinity and selectivity to quadruplex DNA was observed.

Dynamic DNA Templates for Gold Nanoparticle Discrete Structures:  Control of Geometry, Particle Identity, Write /Erase and Structural Switching

J. Am. Chem. Soc., 2007, 129, 4130-4131

Highlighted in “Nature Nanotechnology”: “Gold nanoparticles: DNA builds bridges”, 30/3/2007

Faisal Aldaye, Hanadi F. Sleiman

This contribution describes a new method to selectively organize gold nanoparticles into libraries of discrete and well-defined structures, using a small set of DNA templates.  Moreover, these structures are addressable post-assembly, and can undergo structural switching and write/erase functions withspecific external agents.  Gold nanoparticle assemblies hold promise as new materials for catalysis, sensing, as well as nanoelectronic and nanophotonic applications.  Many of their properties depend on the relative arrangement of the particles within the assembly. For example, their ability for single electron transport may lead to the design of nanoparticle-based alternatives to traditional silicon-based electronic components.  As well, they can significantly enhance the electromagnetic field in particular locations, and can potentially be used for the design of plasmon superemitters and surface-enhanced Raman (SERS) substrates.  However, fundamental studies of these properties have been hampered by the lack of systematic methods to assemble them into well-defined discrete model structures.  As a result, many of these properties (e.g., SERS “hot spots”) have been generated in an empirical fashion using extended two- or three-dimensional assemblies.  In the present method, single stranded, cyclic DNA templates that possess rigid organic vertices are used to precisely position gold nanoparticles that are singly labeled with DNA into discrete structures.  Control of geometry is shown by the ready creation of triangles and squares of nanoparticles.  Modularity is shown by the precise assembly of large and small particles into triangles of all combinations.  Structural switching is demontrated by the use of a square DNA template to assemble nanoparticles into squares, trapezoids and rectangles.  Finally, write/erase function is established by the assembly of a triangle of three gold nanoparticles, the selective removal of one of these particles, and the re-writing of a different nanoparticle within this assemblies.  Overall, this represents what is, to our knowledge, the highest level of control over the assembly of nanoparticles.

Luminescent Vesicles, Tubules, Bowls and Star Micelles from Ruthenium Bipyridine Block Copolymers

Macromolecules, 2007, 40, 3733-3738

Kimberly Metera, Hanadi F. Sleiman

We report the first detailed study on the self-assembly of diblock copolymers containing the luminescent metal complex Ru(bpy)32+, which were constructed by ring-opening metathesis polymerization.  Control over the block length, overall polymer length, polymer concentration and solution conditions has led to the reproducible formation of a number of solution morphologies including vesicles, tubules, large compound micelles, star micelles, and bowls, which all contain Ru(bpy)32+ within the micellar core/vesicle wall.  These morphologies hold interesting potential for the facile organization of architectures useful in catalysis and light harvesting.

DNA-Protein Non-Covalent Crosslinking: Ruthenium Dipyridophenazine Biotin Complex for the Assembly of Proteins and Gold Nanoparticles on DNA Templates

ChemBioChem, 2007, 8, 804-812

M. Slim, N. Durisic, P. Grutter, H. F. Sleiman

 

We report the first example of a small molecule which can non-covalently crosslink DNA with streptavidin and streptavidin-labeled materials.  The crosslinking ability of molecule 1 was used to template the assembly of streptavidin molecules on a plasmid circular DNA, as visualized by atomic force microscopy.  In addition, we show the organization of discrete groupings of gold nanoparticles labeled with streptavidin on a linear DNA template of finite size, using 1 (transmission electron microscopy), with the DNA template acting as a “molecular ruler” to dictate the number of particles in the assembly.  Overall, this work allows the facile, modular and potentially selective assembly of a large number of readily obtainable streptavidin- or biotin-labeled materials on DNA templates. 

Molecule-Responsive Block Copolymer Micelles

Chemistry, a European Journal , 2007, 13, 4560-4570

 Y. Ishihara, H. S. Bazzi, V. Toader, F. Godin, H. F. Sleiman

This manuscript describes the first example of a block copolymer micelle, which can selectively recognize a complementary small molecule, with concomitant opening and complete deaggregation of this micelle.  Environmentally responsive block copolymer micelles have been extensively investigated as selective drug delivery vehicles, as well as templates for nanopatterning of materials.  Stimuli that have been used in the literature have been pH, ionic strength, temperature, oxidation and light irradiation.  However, to the best of our knowledge, this is the first example of a block copolymer micelle which shows a dramatic macroscopic response to the addition of a specific small molecule, with high selectivity.  Many applications can be anticipated for these polymeric micelles, including selective drug delivery in a biological environment where a specific molecule is overexpressed, molecular sensors, which translate a molecular recognition event into a large change in light scattering properties, as well as materials for the orthogonal patterning of surfaces using specific small molecules. 

Sequential Self-Assembly of a DNA Hexagon as a Template for the Organization of Gold Nanoparticles

Angew. Chem. Int. Ed. 2006, 45, 2204-2209.

Faisal A. Aldaye & Hanadi F. Sleiman

A cyclic hexamer of six gold nanoparticles was sequentially and selectively self-assembled by labeling each particle (red sphere) with a DNA-containing molecule (colored block), which serves to dictate their ultimate location within the final construct. This method may be used to construct any discrete well-defined pattern of nanoparticles.

This contribution was selected by the editors as a ‘hot paper’ and received its own cover page.