Sequence-Defined DNA Polymers: New Tools for DNA Nanotechnology and Nucleic Acid Therapy.

ConspectusStructural DNA nanotechnology offers a unique self-assembly toolbox to construct soft materials of arbitrary complexity, through bottom-up approaches including DNA origami, brick, wireframe, and tile-based assemblies. This toolbox can be expanded by incorporating interactions orthogonal to DNA base-pairing such as metal coordination, small molecule hydrogen bonding, π-stacking, fluorophilic interactions, or the hydrophobic effect. These interactions allow for hierarchical and long-range organization in DNA supramolecular assemblies through a DNA-minimal approach: the use of fewer unique DNA sequences to make complex structures.

Heat-activated growth of metastable and length-defined DNA fibers expands traditional polymer assembly.

Biopolymers such as nucleic acids and proteins exhibit dynamic backbone folding, wherein site-specific intramolecular interactions determine overall structure. Proteins then hierarchically assemble into supramolecular polymers such as microtubules, that are robust yet dynamic, constantly growing or shortening to adjust to cellular needs. The combination of dynamic, energy-driven folding and growth with structural stiffness and length control is difficult to achieve in synthetic polymer self-assembly.

Divergent Polymer Superstructures from Protonated Poly(adenine) DNA and RNA.

Studies have shown that poly(adenine) DNA and RNA strands protonate at a low pH to form self-associating duplexes; however, the nanoscopic morphology of these structures is unclear. Here, we use Transition Electron Microscopy (TEM), Atomic Force Microscopy (AFM), dynamic light scattering (DLS), and fluorescence spectroscopy to show that both ribose identity (DNA or RNA) and assembly conditions (thermal or room-temperature annealing) dictate unique hierarchical structures for poly(adenine) sequences at a low pH. We show that while the thermodynamic product of protonating poly(adenine) DNA is a discrete dimer of two DNA strands, the kinetic product is a supramolecular polymer that branches and aggregates to form micron-diameter superstructures.

Light-Activated Assembly of DNA Origami into Dissipative Fibrils.

Hierarchical DNA nanostructures offer programmable functions at scale, but making these structures dynamic, while keeping individual components intact, is challenging. Here we show that the DNA A-motif-protonated, self-complementary poly(adenine) sequences-can propagate DNA origami into one-dimensional, micron-length fibrils. When coupled to a small molecule pH regulator, visible light can activate the hierarchical assembly of our DNA origami into dissipative fibrils.

Programming rigidity into size-defined wireframe DNA nanotubes.

Nanotubes built from DNA hold promise for several biological and materials applications, due to their high aspect ratio and encapsulation potential. A particularly appealing goal is to control the size, shape, and dynamic behaviour of DNA nanotubes with minimal design alteration, as nanostructures of varying morphologies and lengths have been shown to exhibit distinct cellular uptake, encapsulation behaviour, and biodistribution. Herein, we report a systematic investigation, combining experimental and computational design, to modulate the length, flexibility, and longitudinal patterns of wireframe DNA nanotubes.

Modulating the Lifetime of DNA Motifs Using Visible Light and Small Molecules.

Here we regulate the formation of dissipative assemblies built from DNA using a merocyanine photoacid that responds to visible light. The operation of our system and the relative distribution of species within it are controlled by irradiation time, initial pH value, and the concentration of a small-molecule binder that inhibits the reaction cycle. This approach is modular, does not require DNA modification, and can be used for several DNA sequences and lengths.

DNA Sequence and Length Dictate the Assembly of Nucleic Acid Block Copolymers.

The self-assembly of block copolymers is often rationalized by structure and microphase separation; pathways that diverge from this parameter space may provide new mechanisms of polymer assembly. Here, we show that the sequence and length of single-stranded DNA directly influence the self-assembly of sequence-defined DNA block copolymers. While increasing the length of DNA led to predictable changes in self-assembly, changing only the sequence of DNA produced three distinct structures: spherical micelles (spherical nucleic acids, SNAs) from flexible poly(thymine) DNA, fibers from semirigid mixed-sequence DNA, and networked superstructures from rigid poly(adenine) DNA.

Incorporation of a Phosphino(pyridine) Subcomponent Enables the Formation of Cages with Homobimetallic and Heterobimetallic Vertices.

Biological systems employ multimetallic assemblies to achieve a range of functions. Here we demonstrate the preparation of metal-organic cages that contain either homobimetallic or heterobimetallic vertices. These vertices are constructed using 2-formyl-6-diphenylphosphinopyridine, which forms ligands that readily bridge between a pair of metal centers, thus enforcing the formation of bimetallic coordination motifs.

Asymmetric patterning drives the folding of a tripodal DNA nanotweezer.

DNA tweezers have emerged as powerful devices for a wide range of biochemical and sensing applications; however, most DNA tweezers consist of single units activated by DNA recognition, limiting their range of motion and ability to respond to complex stimuli. Herein, we present an extended, tripodal DNA nanotweezer with a small molecule junction. Simultaneous, asymmetric elongation of our molecular core is achieved using polymerase chain reaction (PCR) to produce length- and sequence-specific DNA arms with repeating DNA regions.

A dissipative pathway for the structural evolution of DNA fibres.

Biochemical networks interconnect, grow and evolve to express new properties as different chemical pathways are selected during a continuous cycle of energy consumption and transformation. In contrast, synthetic systems that push away from equilibrium usually return to the same self-assembled state, often generating waste that limits system recyclability and prevents the formation of adaptable networks. Here we show that annealing by slow proton dissipation selects for otherwise inaccessible morphologies of fibres built from DNA and cyanuric acid.

Oxidation triggers guest dissociation during reorganization of an Fe L twisted parallelogram.

A three-dimensional Fe L parallelogram was prepared from ferrocene-containing ditopic ligands. The steric preference of the bulky ferrocene cores towards meridional vertex coordination brought about this new structure type, in which the ferrocene units adopt three distinct conformations. The structure possesses two distinct, bowl-like cavities that host anionic guests.

A poly(thymine)-melamine duplex for the assembly of DNA nanomaterials.

The diversity of DNA duplex structures is limited by a binary pair of hydrogen-bonded motifs. Here we show that poly(thymine) self-associates into antiparallel, right-handed duplexes in the presence of melamine, a small molecule that presents a triplicate set of the hydrogen-bonding face of adenine. X-ray crystallography shows that in the complex two poly(thymine) strands wrap around a helical column of melamine, which hydrogen bonds to thymine residues on two of its three faces.

Single-molecule methods in structural DNA nanotechnology.

Single molecules can now be visualised with unprecedented precision. As the resolution of single-molecule experiments improves, so too does the breadth, quantity and quality of information that can be extracted using these methodologies. In the field of DNA nanotechnology, we use programmable interactions between nucleic acids to generate complex, multidimensional structures.

Narcissistic, Integrative, and Kinetic Self-Sorting within a System of Coordination Cages.

Many useful principles of self-assembly have been elucidated through studies of systems where multiple components combine to create a single structure. More complex systems, where multiple product structures self-assemble in parallel from a shared set of precursors, are also of great interest, as biological systems exhibit this behavior. The greater complexity of such systems leads to an increased likelihood that discrete species will not be formed, however.

Conformational Control in Main Group Phosphazane Anion Receptors and Transporters.

Anion binding by receptor molecules is a central field of modern chemistry which impacts areas of catalysis as well as biological and materials chemistry. As binding often requires high chemical stability under aerobic and aqueous conditions for practical applications, carbon-based anion receptors have dominated this field, with main group element analogues receiving far less attention. The recent observation that the air- and moisture-stable amino-cyclophosph(V)azanes of the type [RN(E)P(μ-NR)] (E = O, S, Se) can exhibit halide binding that is competitive with topologically related organic receptors (such as squaramides and thioureas) has motivated us here to explore how the binding properties of phosphazane receptors can be enhanced further.

Transition-Metal-Functionalized DNA Double-Crossover Tiles: Enhanced Stability and Chirality Transfer to Metal Centers.

The double crossover junction (DX) is a fundamental building block for generating complex and varied structures from DNA. However, its implementation in functional devices is limited to the inherent properties of DNA itself. Here, we developed design strategies to generate the first metal-DX DNA tiles (DX ) by site-specifically functionalizing the tile crossovers with tetrahedral binding pockets that coordinate Cu .

Remote control of charge transport and chiral induction along a DNA-metallohelicate.

Herein we present a new strategy to achieve chiral induction and redox switching along the backbone of metallohelicate architectures, wherein a DNA duplex directs the handedness and charge transport properties of a metal-organic assembly more than 60 bonds away (a distance of >10 nm). The quantitative and site-specific binding of copper(i) ions to DNA-templated coordination sites imparts enhanced thermodynamic stability to the assembly, while the DNA duplex transfers its natural right-handed helicity to the proximal and distal metal centers of the helicates. When copper(ii) ions are employed instead of copper(i) ions, spontaneous DNA-mediated reduction occurs, which we propose is followed by a slower change in coordination environment (from pentacoordinate CuII to tetrahedral CuI) to generate copper(i) helicates.

Guest Binding via N-H⋅⋅⋅π Bonding and Kinetic Entrapment by an Inorganic Macrocycle.

Modern supramolecular chemistry is overwhelmingly based on non-covalent interactions involving organic architectures. However, the question of what happens when you depart from this area to the supramolecular chemistry of structures based on non-carbon frameworks remains largely unanswered, and is an area that potentially provides new directions in molecular activation, host-guest chemistry, and biomimetic chemistry. In this work, we explore the unusual host-guest chemistry of the pentameric macrocycle [{P(μ-N Bu} NH] with a range of anionic and neutral guests.

Multisite Binding of Drugs and Natural Products in an Entropically Favorable, Heteroleptic Receptor.

The cavities of artificial receptors are defined by how their components fit together. The encapsulation of specific molecules can thus be engineered by considering geometric principles; however, intermolecular interactions and steric fit scale with receptor size, such that the ability to bind multiple guests from a specific class of compounds remains a current challenge. By employing metal-organic self-assembly, we have prepared a triangular prism from two different ligands that is capable of binding more than 20 different natural products, drugs, and steroid derivatives within its prolate cavity.

Fluorometric Recognition of Nucleotides within a Water-Soluble Tetrahedral Capsule.

The design of aqueous probes and binders for complex, biologically relevant anions presents a key challenge in supramolecular chemistry. Herein, a tetrahedral assembly with cationic faces and corners is reported that is capable of discriminating between anionic and neutral guests in water. Electrostatic repulsion between subcomponents can be overcome by the addition of an anionic template, or generating a robust covalent framework by incorporating tris(2-aminoethyl)amine (TREN).

Hydrogen-Bond-Assisted Symmetry Breaking in a Network of Chiral Metal-Organic Assemblies.

Herein we elucidate the interplay of chiral, chelate, solvent, and hydrogen-bonding information in the self-assembly of a series of new three-dimensional metal-organic architectures. Enantiopure ligands, each containing H-bond donors and acceptors, form different structures, depending on the ratio in which they are combined: enantiopure components form ML assemblies, whereas racemic mixtures form ML stacks. Chiral amplification within ML enantiomers was observed when a 2:1 ratio of R and S subcomponent enantiomers was employed.

Otherwise Unstable Structures Self-Assemble in the Cavities of Cuboctahedral Coordination Cages.

We present a method for the directed self-assembly of interlocked structures and coordination complexes in a set of metal-organic hosts. New homo- and heteroleptic metal complexes-species that cannot be prepared outside-form within the cavities of cuboctahedral coordination cages. When linear bidentate guests and macrocycles are sequentially introduced to the host, a rotaxane is threaded internally; the resulting ternary host-guest complex is a new kind of molecular gyroscope.

Quantified structural speciation in self-sorted CoII6L cage systems.

The molecular components of biological systems self-sort in different ways to function cooperatively and to avoid interfering with each other. Understanding the driving forces behind these different sorting modes enables progressively more complex self-assembling synthetic systems to be designed. Here we show that subtle ligand differences engender distinct ML cage geometries - an -symmetric scalenohedron, or pseudo-octahedra having point symmetry.

Formation and selection of the macrocycle [{(BuN[double bond, length as m-dash])P(μ-NBu)}(μ-Se){P(μ-NBu)}].

Main group inorganic macrocycles, based on p-block element backbones other than carbon, are a challenging synthetic target that has been largely overlooked. In this study, we show that a simple strategy based on the combination of electrophilic and nucleophilic phosphazane building blocks can be extended to readily accessible [E(tBuN)P(μ-NtBu)]22- nucleophilic components, as exemplified by the Se-bridge PIII/PV phosphazane macrocycle [{(tBuN[double bond, length as m-dash])PV(μ-NtBu)}2(μ-Se)2{PIII(μ-NtBu)}2]3.

How Changing the Bridgehead Can Affect the Properties of Tripodal Ligands.

Although a multitude of studies have explored the coordination chemistry of classical tripodal ligands containing a range of main-group bridgehead atoms or groups, it is not clear how periodic trends affect ligand character and reactivity within a single ligand family. A case in point is the extensive family of neutral tris-2-pyridyl ligands E(2-py) (E=C-R, N, P), which are closely related to archetypal tris-pyrazolyl borates. With the 6-methyl substituted ligands E(6-Me-2-py) (E=As, Sb, Bi) in hand, the effects of bridgehead modification alone on descending a single group in the periodic table were assessed.