Structure and Properties of DNA-Based Reversible Polymers

RNA Nanoparticles as Rubber for Compelling Vessel Extravasation to Enhance Tumor Targeting and for Fast Renal Excretion to Reduce Toxicity

Rubber is a fascinating material in both industry and daily life. The development of elastomeric material in nanotechnology is imperative due to its economic and technological potential. By virtue of their distinctive physicochemical properties, nucleic acids have been extensively explored in material science. The Phi29 DNA packaging motor contains a 3WJ with three angles of 97°, 125°, and 138°. Here, the rubber-like property of RNA architectures was investigated using optical tweezers and in vivo imaging technologies. The 3WJ 97° interior angle was contracted or stretched to 60°, 90°, and 108° at will to build elegant RNA triangles, squares, pentagons, cubes, tetrahedrons, dendrimers, and prisms. RNA nanoarchitecture was stretchable and shrinkable by optical tweezer with multiple extension and relaxation repeats like a rubber. Comparing to gold and iron nanoparticles with the same size, RNA nanoparticles display stronger cancer-targeting outcomes, while less accumulation in healthy organs. Generally, the upper limit of renal excretion is 5.5 nm; however, the 5, 10, and 20 nm RNA nanoparticles passed the renal filtration and resumed their original structure identified in urine. These findings solve two previous mysteries: (1) Why RNA nanoparticles have an unusually high tumor targeting efficiency since their rubber or amoeba-like deformation property enables them to squeeze out of the leaky vasculature to improve the EPR effect; and (2) why RNA nanoparticles remain non-toxic since they can be rapidly cleared from the body via renal excretion into urine with little accumulation in the body. Considering its controllable shape and size plus its rubber-like property, RNA holds great promises for industrial and biomedical applications especially in cancer therapeutics delivery.

Programming Protein Polymerization with DNA

A strategy that utilizes DNA for controlling the association pathway of proteins is described. This strategy uses sequence-specific DNA interactions to program energy barriers for polymerization, allowing for either step-growth or chain-growth pathways to be accessed. Two sets of mutant green fluorescent protein (mGFP)-DNA monomers with single DNA modifications have been synthesized and characterized. Depending on the deliberately controlled sequence and conformation of the appended DNA, these monomers can be polymerized through either a step-growth or chain-growth pathway. Cryo-electron microscopy with Volta phase plate technology enables the visualization of the distribution of the oligomer and polymer products, and even the small mGFP-DNA monomers. Whereas cyclic and linear polymer distributions were observed for the step-growth DNA design, in the case of the chain-growth system linear chains exclusively were observed, and a dependence of the chain length on the concentration of the initiator strand was noted. Importantly, the chain-growth system possesses a living character whereby chains can be extended with the addition of fresh monomer. This work represents an important and early example of mechanistic control over protein assembly, thereby establishing a robust methodology for synthesizing oligomeric and polymeric protein-based materials with exceptional control over architecture.

Supramolecular Properties of a Monocarboxylic Acid-Functionalized "Texas-Sized" Molecular Box

A new carboxylic acid-functionalized "Texas-sized" molecular box TxSB-CO₂H has been prepared by combining two separate building blocks via an iodide-catalyzed macrocyclization reaction. A single-crystal X-ray diffraction analysis revealed a paired "clip-like" dimer in the solid state. Concentration-dependent behavior is seen for samples of TxSB-CO₂H as prepared, as inferred from ¹H NMR spectroscopic studies carried out in DMSO- d₆. However, in the presence of excess acid (1% by weight of deuterated trifluoracetic acid; TFA- d₁), little evidence of aggregation is seen in DMSO- d₆ except at the highest accessible concentrations. In contrast, the conjugate base form, TxSB-CO₂^-, produced in situ via the addition of excess triethylamine to DMSO- d₆ solutions of TxSB-CO₂H acts as a self-complementary monomer that undergoes self-assembly to stabilize a formal oligomer ([TxSB-CO₂^-] _n) with a degree of polymerization of approximately 5-6 at a concentration of 70 mM. Evidence in support of the proposed oligomerization of TxSB-CO₂^- in solution and in the solid state came from one- and two-dimensional ¹H NMR spectroscopy, X-ray crystallography, dynamic light scattering (DLS), and scanning electron microscopy (SEM). A series of solution-based analyses carried out in DMSO and DMSO- d₆ provide support for the notion that the self-assembled constructs produced from TxSB-CO₂^- are responsive to environmental stimuli, including exposure to the acetate anion (as its tetrabutylammonium, TBA⁺, salt), and changes in overall concentration, temperature, and protonation state. The resulting transformations are thought to reflect the reversible nature of the underlying noncovalent interactions. They also permit the stepwise interconversion between TxSB-CO₂H and [TxSB-CO₂^-] _n via the sequential addition of triethylamine and TFA- d₁. The present work thus serves to illustrate how appropriately functionalized molecular box-type macrocycles may be used to develop versatile stimuli-responsive materials. It also highlights how aggregated forms seen in the solid state are not necessarily retained under competitive solution-phase conditions.

Supramolecular Polymers Based on Non-Coplanar AAA-DDD Hydrogen-Bonded Complexes

Non-coplanar triple-hydrogen-bond arrays are connected as telechelic groups to alkyl chains and their properties as AA/BB type supramolecular polymers are examined. Viscosity studies at three temperatures are used to study the ring-chain equilibrium and determine the critical concentrations where polymer chains are formed. It is observed that neither the temperature range studied nor the alkyl chain length of one component significantly affect the polymerization properties in this system.

Tailoring length and viscosity of dynamic metallo-supramolecular polymers in solution

We present a detailed study of metallo-supramolecular coordination polymers (MEPEs) and how to adjust their chain-length and viscosity. A model is established, which can easily be used to prepare MEPEs of desired average molecular weight.

Bioinspired affinity DNA polymers on nanoparticles for drug sequestration and detoxification

Nanomaterials with the ability of sequestering target molecules hold great potential for a variety of applications. To ensure the stable sequestration, most of these nanomaterials have been traditionally designed with a clear boundary or compact structures and behave as closed systems. While this feature is beneficial to applications such as drug delivery, it may pose a challenge to applications where fast molecular transport from the environment to nanomaterials is critical. Thus, this study was aimed at exploring a nanomaterial with affinity DNA polymers and nanoparticles as an open system with function similar to jellyfish tentacles in sequestering target molecules from surroundings. The results show that this nanomaterial can effectively and rapidly sequester both small molecule drugs and large molecule biologics and resultantly mitigate their biological effects. Thus, this nanomaterial holds potential as a universal nanoscale antidote for drug removal and detoxification. While this nanomaterial was evaluated by using drug removal and detoxification as a model, the synthesis of periodically oriented affinity polymers on a nanoparticle with the capability of sequestering target molecules may be tuned for broad applications such as separation, sensing, imaging and drug delivery.

Construction of three-dimensional DNA hydrogels from linear building blocks

A three-dimensional DNA hydrogel was generated by self-assembly of short linear double-stranded DNA (dsDNA) building blocks equipped with sticky ends. The resulting DNA hydrogel is thermoresponsive and the length of the supramolecular dsDNA structures varies with temperature. The average diffusion coefficients of the supramolecular dsDNA structures formed by self-assembly were determined by diffusion-ordered NMR spectroscopy (DOSY NMR) for temperatures higher than 60 °C. Temperature-dependent rheological measurements revealed a gel point of 42±1 °C. Below this temperature, the resulting material behaved as a true gel of high viscosity with values for the storage modulus G' being significantly larger than that for the loss modulus G''. Frequency-dependent rheological measurements at 20 °C revealed a mesh size (ξ) of 15 nm. AFM analysis of the diluted hydrogel in the dry state showed densely packed structures of entangled chains, which are also expected to contain multiple interlocked rings and catenanes.

Binding and supramolecular organization of homo- and heterotelechelic oligomers in solutions

Solvent can subtly influence the organization of supramolecular polymers.

Self-healing biomaterials

The goal of this review is to introduce the biomaterials community to the emerging field of self-healing materials, and also to suggest how one could utilize and modify self-healing approaches to develop new classes of biomaterials. A brief discussion of the in vivo mechanical loading and resultant failures experienced by biomedical implants is followed by presentation of the self-healing methods for combating mechanical failure. If conventional composite materials that retard failure may be considered zeroth generation self-healing materials, then taxonomically speaking, first generation self-healing materials describe approaches that "halt" and "fill" damage, whereas second generation self-healing materials strive to "fully restore" the prefailed material structure. In spite of limited commercial use to date, primarily because the technical details have not been suitably optimized, it is likely from a practical standpoint that first generation approaches will be the first to be employed commercially, whereas second generation approaches may take longer to implement. For self-healing biomaterials the optimization of technical considerations is further compounded by the additional constraints of toxicity and biocompatibility, necessitating inclusion of separate discussions of design criteria for self-healing biomaterials.

Breaking Down the Supramolecular Ensemble: Single-Molecule Studies of the Concentration Dependence of Main-Chain Supramolecular Polymer Molecular Weight Distributions on Surfaces

Single molecule atomic force microscopy (AFM) studies of oligonucleotide-based supramolecular polymers on surfaces are used to examine the molecular weight distribution of the polymers formed between a functionalized surface and an AFM tip as a function of monomer concentration. For the concentrations examined here, excellent agreement with a multi-stage open association model of polymerization is obtained, without the need to invoke additional contributions from secondary steric interactions at the surface.

Distance dependent interhelical couplings of organic rods incorporated in DNA 4-helix bundles

The synthesis of a conjugated linear organic module containing terminal salicylaldehyde groups and a central activated ester, designed for conjugation to amino-modified oligonucleotides, is presented. The organic module has a phenylene-ethynylene backbone and is highly fluorescent. It is conjugated to oligonucleotide sequences and incorporated into specific locations in a well-defined DNA 4-helix bundle (4-HB). The DNA-nanostructure offers precise location control of the organic modules which allows for selective interhelical coupling reactions. In this study, metal-salen formation as well as dihydrazone formation are used to covalently interlink the organic modules. Both coupling reactions are highly dependent on the distances between the organic modules in the 4-HB. Neighboring modules dimerize easier, whereas more distanced modules are less prone to react, even when the linkers are extended. The dimeric products are characterized by denaturing polyacrylamide gel electrophoresis (PAGE), high performance liquid chromatography (HPLC), and matrix assisted laser desorption/absorption ionization time-of-flight (MALDI TOF) mass spectrometry.

Pyromellitamide gelators: exponential rate of aggregation, hierarchical assembly, and their viscoelastic response to anions

The gelation and aggregation properties of a newly synthesized structurally simplified tetrahexyl pyromellitamide 2 have been studied and compared to the previously reported tetra(ethylhexanoate) pyromellitide 1, indicating that the ester groups in the latter significantly impede its aggregation. Morphology studies (AFM and TEM) on the aggregates formed by tetrahexyl pyromellitamide 2 in cyclohexane revealed highly uniform aggregates with different dimensions at different starting concentrations, suggesting that this molecule aggregates in a hierarchical fashion from a one-dimensional supramolecular polymer through hollow tubes or compressed helices to a network structure and then to a gel. This hypothesis is further supported by viscosity measurements that indicate a crossover point where individual supramolecular fibers get entangled at concentrations above ca. 3 mM in cyclohexane. Addition of 1 equiv of tetraalkylammonium salts of chloride or bromide, however, caused the viscosities of these pyromellitamide solutions to drop by a factor of 2-3 orders of magnitude, demonstrating the sensitivity of these aggregates to the presence of small anions. The sensitivity to anions does depend on the solubility of the salts used as small anion salts with little solubility in cyclohexane did not show this effect. Time-dependent viscosity studies showed that the aggregation of pyromellitamide 2 follows an exponential rate law, possibly related to the columnar rearrangements that are associated with the observed 6 angstroms contraction in d spacing in the XRD pattern of these gels. These results, particularly on the importance of kinetics of aggregation of self-assembled pyromellitamide gels, will be useful for future development of related materials for a number of applications, including tissue engineering and drug delivery.

Single-Molecule Force Spectroscopy of DNA-Based Reversible Polymer Bridges: Surface Robustness and Homogeneity

Single-molecule force spectroscopy, as implemented in an atomic force microscope, provides a rarely-used method by which to monitor dynamic processes that occur near surfaces. Here, a methodology is presented and characterized that facilitates the study of polymer bridging across nanometer-sized gaps. The model system employed is that of DNA-based reversible polymers, and an automated procedure is introduced that allows the AFM tip-surface contact point to be automatically determined, and the distance d between opposing surfaces to be actively controlled. Using this methodology, the importance of several experimental parameters was systematically studied, e.g. the frequency of repeated tip/surface contacts, the area of the substrate surface sampled by the AFM, and the use of multiple AFM tips and substrates. Experiments revealed the surfaces to be robust throughout pulling experiments, so that multiple touches and pulls could be carried out on a single spot with no measurable affect on the results. Differences in observed bridging probabilities were observed, both on different spots on the same surface and, more dramatically, from one day to another. Data normalization via a reference measurement allows data from multiple days to be directly compared.

Thermodynamic description of bis-urea self-assembly: competition between two supramolecular polymers

Supramolecular polymers are chains of small molecules held together through reversible noncovalent interactions. In general, a given monomer self-assembles into a single type of supramolecular polymer. However, in a few cases, two different self-assembled structures can coexist; this yields interesting responsive systems. To improve the understanding of these systems, we report an association model describing the self-assembly of a supramolecular polymer into two competing forms. The parameters controlling the system were measured by high sensitivity differential scanning calorimetry and isothermal titration calorimetry in the case of a hydrogen-bonded bis-urea supramolecular polymer solution in toluene. The model enables us to compute the proportion and length of all components in the system at any temperature and concentration. The results of these calculations are in agreement with the experimental phase diagram and with independent viscosity measurements.

On the Characterization of Dynamic Supramolecular Systems: A General Mathematical Association Model for Linear Supramolecular Copolymers and Application on a Complex Two-Component Hydrogen-Bonding System

A general mathematical model for the characterization of the dynamic (kinetically labile) association of supramolecular assemblies in solution is presented. It is an extension of the equal K (EK) model by the stringent use of linear algebra to allow for the simultaneous presence of an unlimited number of different units in the resulting assemblies. It allows for the analysis of highly complex dynamic equilibrium systems in solution, including both supramolecular homo- and copolymers without the recourse to extensive approximations, in a field in which other analytical methods are difficult. The derived mathematical methodology makes it possible to analyze dynamic systems such as supramolecular copolymers regarding for instance the degree of polymerization, the distribution of a given monomer in different copolymers as well as its position in an aggregate. It is to date the only general means to characterize weak supramolecular systems. The model was fitted to NMR dilution titration data by using the program Matlab, and a detailed algorithm for the optimization of the different parameters has been developed. The methodology is applied to a case study, a hydrogen-bonded supramolecular system, salen 4+porphyrin 5. The system is formally a two-component system but in reality a three-component system. This results in a complex dynamic system in which all monomers are associated to each other by hydrogen bonding with different association constants, resulting in homo- and copolymers 4n5m as well as cyclic structures 6 and 7, in addition to free 4 and 5. The system was analyzed by extensive NMR dilution titrations at variable temperatures. All chemical shifts observed at different temperatures were used in the fitting to obtain the DeltaH degrees and DeltaS degrees values producing the best global fit. From the derived general mathematical expressions, system 4+5 could be characterized with respect to above-mentioned parameters.

Non-covalent polymer assembly using arrays of hydrogen-bonds

Hydrogen-bond-mediated non-covalent polymer synthesis is an emerging area that presents new opportunities for the design of stimuli-responsive materials. Central to this is the ready availability of appropriate building blocks with which to link monomers together. This review discusses recent developments in the design, synthesis and use of arrays of hydrogen-bonds as supramolecular linking units.

Physical organic chemistry of supramolecular polymers

Unlike the case of traditional covalent polymers, the entanglements that determine properties of supramolecular polymers are defined by very specific, intermolecular interactions. Recent work using modular molecular platforms to probe the mechanisms underlying mechanical response of supramolecular polymers is reviewed. The contributions of supramolecular kinetics, thermodynamics, and conformational flexibility to supramolecular polymer properties in solutions of discrete polymers, in networks, and at interfaces, are described. Molecule-to-material relationships are established through methods reminiscent of classic physical organic chemistry.

A modular approach toward block copolymers

A novel methodology for the formation of block copolymers has been developed that combines ring-opening metathesis polymerization (ROMP) with functional chain-transfer agents (CTAs) and self-assembly. Telechelic homopolymers of cyclooctene derivatives end-functionalized with hydrogen-bonding or metal-coordination sites are formed through the combination of ROMP with a corresponding functional CTA. These telechelic homopolymers are fashioned with a high control over molecular weight and without the need for post-polymerization procedures. The homopolymers undergo fast and efficient self-assembly with their complement homopolymer or small molecule analogue to form block-copolymer architectures. The block copolymers show equivalent association constants as their small molecule analogues described in the literature, regardless of size or nature of the complementary unit or the polymer side chain.

Liquid-Crystalline Supramolecular Polymers Formed through Complementary Nucleobase-Pair Interactions

We report how the placement of nucleobase units, thymine, or N6-(4-methoxybenzoyl)adenine, onto the ends of a mesogenic core, bis-4-alkoxy-substituted bis(phenylethynyl)benzene, affects the properties of these materials. We show that addition of these bulky polar groups significantly reduces the range of liquid-crystalline behavior of these compounds. However, mixing two complementary nucleobase-containing AA- and BB-type monomer units together does result in the formation of stable, thermotropic liquid-crystalline (LC) phases. Hydrogen bonding is shown to play an important role in the formation of these LC phases, consistent with the formation of oligomeric or polymeric hydrogen-bonded aggregates. X-ray analyses of these mixed materials are consistent with the formation of smectic C phases.

DNA-programmed assembly of nanostructures

DNA is a unique material for nanotechnology since it is possible to use base sequences to encode instructions for assembly in a predetermined fashion at the nanometre scale. Synthetic oligonucleotides are readily obtained by automated synthesis and numerous techniques have been developed for conjugating DNA with other materials. The exact spatial positioning of materials is crucial for the future development of complex nanodevices and the emerging field of DNA-nanotechnology is now exploring DNA-programmed processes for the assembly of organic compounds, biomolecules, and inorganic materials.