Accelerating DNA-Based Computing on a Supramolecular Polymer.
ABSTRACT: Dynamic DNA-based circuits represent versatile systems to perform complex computing operations at the molecular level. However, the majority of DNA circuits relies on freely diffusing reactants, which slows down their rate of operation substantially. Here we introduce the use of DNA-functionalized benzene-1,3,5-tricarboxamide (BTA) supramolecular polymers as dynamic scaffolds to template DNA-based molecular computing. By selectively recruiting DNA circuit components to a supramolecular BTA polymer functionalized with 10-nucleotide handle strands, the kinetics of strand displacement and strand exchange reactions were accelerated 100-fold. In addition, strand exchange reactions were also favored thermodynamically by bivalent interactions between the reaction product and the supramolecular polymer. The noncovalent assembly of the supramolecular polymers enabled straightforward optimization of the polymer composition to best suit various applications. The ability of supramolecular BTA polymers to increase the efficiency of DNA-based computing was demonstrated for three well-known and practically important DNA-computing operations: multi-input AND gates, Catalytic Hairpin Assembly and Hybridization Chain Reactions. This work thus establishes supramolecular BTA polymers as an efficient platform for DNA-based molecular operations, paving the way for the construction of autonomous bionanomolecular systems that confine and combine molecular sensing, computation, and actuation.
Project description:Nature uses dynamic molecular platforms for the recruitment of weakly associating proteins into higher-order assemblies to achieve spatiotemporal control of signal transduction. Nanostructures that emulate this dynamic behavior require features such as plasticity, specificity and reversibility. Here we introduce a synthetic protein recruitment platform that combines the dynamics of supramolecular polymers with the programmability offered by DNA-mediated protein recruitment. Assembly of benzene-1,3,5-tricarboxamide (BTA) derivatives functionalized with a 10-nucleotide receptor strand into µm-long supramolecular BTA polymers is remarkably robust, even with high contents of DNA-functionalized BTA monomers and associated proteins. Specific recruitment of DNA-conjugated proteins on the supramolecular polymer results in a 1000-fold increase in protein complex formation, while at the same time enabling their rapid exchange along the BTA polymer. Our results establish supramolecular BTA polymers as a generic protein recruitment platform and demonstrate how assembly of protein complexes along the supramolecular polymer allows efficient and dynamic control of protein activity.
Project description:Controlling the reciprocity between chemical reactivity and supramolecular structure is a topic of great interest in the emergence of molecular complexity. In this work, we investigate the effect of a covalent reaction as a trigger to depolymerize a supramolecular assembly. We focus on the impact of an in situ thiol–ene reaction on the (co)polymerization of three derivatives of benzene-1,3,5-tricarboxamide (BTA) monomers functionalized with cysteine, hexylcysteine, and alkyl side chains: Cys-BTA, HexCys-BTA, and a-BTA. Long supramolecular polymers of Cys-BTA can be depolymerized into short dimeric aggregates of HexCys-BTAvia the in situ thiol–ene reaction. Analysis of the system by time-resolved spectroscopy and light scattering unravels the fast dynamicity of the structures and the mechanism of depolymerization. Moreover, by intercalating the reactive Cys-BTA monomer into an unreactive inert polymer, the in situ thiol–ene reaction transforms the intercalator into a sequestrator and induces the depolymerization of the unreactive polymer. This work shows that the implementation of reactivity into supramolecular assemblies enables temporal control of depolymerization processes, which can bring us one step closer to understanding the interplay between non-covalent and covalent chemistry. We report on the controlled depolymerization of supramolecular 1D polymers into well-defined dimers triggered by a covalent reaction on the side chains of the monomer.
Project description:Dynamic binding events are key to arrive at functionality in nature, and these events are often governed by electrostatic or hydrophobic interactions. Synthetic supramolecular polymers are promising candidates to obtain biomaterials that mimic this dynamicity. Here, we created four new functional monomers based on the benzene-1,3,5-tricarboxamide (BTA) motif. Choline or atropine groups were introduced to obtain functional monomers capable of competing with the cell wall of <i>Streptococcus pneumoniae</i> for binding of essential choline-binding proteins (CBPs). Atropine-functionalized monomers <b>BTA-Atr</b> and <b>BTA-Atr</b><sub><b>3</b></sub> were too hydrophobic to form homogeneous assemblies, while choline-functionalized monomers <b>BTA-Chol</b> and <b>BTA-Chol</b><sub><b>3</b></sub> were unable to form fibers due to charge repulsion. However, copolymerization of <b>BTA-Chol</b><sub><b>3</b></sub> with non-functionalized <b>BTA-(OH)</b><sub><b>3</b></sub> yielded dynamic fibers, similar to <b>BTA-(OH)</b><sub><b>3</b></sub>. These copolymers showed an increased affinity toward CBPs compared to free choline due to multivalent effects. BTA-based supramolecular copolymers are therefore a versatile platform to design bioactive and dynamic supramolecular polymers with novel biotechnological properties.
Project description:In the field of supramolecular (co)polymerizations, the ability to predict and control the composition and length of the supramolecular (co)polymers is a topic of great interest. In this work, we elucidate the mechanism that controls the polymer length in a two-component cooperative supramolecular polymerization and unveil the role of the second component in the system. We focus on the supramolecular copolymerization between two derivatives of benzene-1,3,5-tricarboxamide (BTA) monomers: a-BTA and Nle-BTA. As a single component, a-BTA cooperatively polymerizes into long supramolecular polymers, whereas Nle-BTA only forms dimers. By mixing a-BTA and Nle-BTA in different ratios, two-component systems are obtained, which are analyzed in-depth by combining spectroscopy and light-scattering techniques with theoretical modeling. The results show that the length of the supramolecular polymers formed by a-BTA is controlled by competitive sequestration of a-BTA monomers by Nle-BTA, while the obvious alternative Nle-BTA acts as a chain-capper is not operative. This sequestration of a-BTA leads to short, stable species coexisting with long cooperative aggregates. The analysis of the experimental data by theoretical modeling elucidates the thermodynamic parameters of the copolymerization, the distributions of the various species, and the composition and length of the supramolecular polymers at various mixing ratios of a-BTA and Nle-BTA. Moreover, the model was used to generalize our results and to predict the impact of adding a chain-capper or a competitor on the length of the cooperative supramolecular polymers under thermodynamic control. Overall, this work unveils comprehensive guidelines to master the nature of supramolecular (co)polymers and brings the field one step closer to applications.
Project description:Multicomponent supramolecular polymers are a versatile platform to prepare functional architectures, but a few studies have been devoted to investigate their noncovalent synthesis. Here, we study supramolecular copolymerizations by examining the mechanism and time scales associated with the incorporation of new monomers in benzene-1,3,5-tricarboxamide (BTA)-based supramolecular polymers. The BTA molecules in this study all contain three tetra(ethylene glycol) chains at the periphery for water solubility but differ in their alkyl chains that feature either 10, 12 or 13 methylene units. C<sub>10</sub>BTA does not form ordered supramolecular assemblies, whereas C<sub>12</sub>BTA and C<sub>13</sub>BTA both form high aspect ratio supramolecular polymers. First, we illustrate that C<sub>10</sub>BTA can mix into the supramolecular polymers based on either C<sub>12</sub>BTA or C<sub>13</sub>BTA by comparing the temperature response of the equilibrated mixtures to the temperature response of the individual components in water. Subsequently, we mix C<sub>10</sub>BTA with the polymers and follow the copolymerization over time with UV spectroscopy and hydrogen/deuterium exchange mass spectrometry experiments. Interestingly, the time scales obtained in both experiments reveal significant differences in the rates of copolymerization. Coarse-grained simulations are used to study the incorporation pathway and kinetics of the C<sub>10</sub>BTA monomers into the different polymers. The results demonstrate that the kinetic stability of the host supramolecular polymer controls the rate at which new monomers can enter the existing supramolecular polymers.
Project description:The use of supramolecular polymers to construct functional biomaterials is gaining more attention due to the tunable dynamic behavior and fibrous structures of supramolecular polymers, which resemble those found in natural systems, such as the extracellular matrix. Nevertheless, to obtain a biomaterial capable of mimicking native systems, complex biomolecules should be incorporated, as they allow one to achieve essential biological processes. In this study, supramolecular polymers based on water-soluble benzene-1,3,5-tricarboxamides (BTAs) were assembled in the presence of hyaluronic acid (HA) both in solution and hydrogel states. The coassembly of BTAs bearing tetra(ethylene glycol) at the periphery (<b>BTA-OEG<sub>4</sub></b>) and HA at different ratios showed strong interactions between the two components that led to the formation of short fibers and heterogeneous hydrogels. BTAs were further covalently linked to HA (<b>HA-BTA</b>), resulting in a polymer that was unable to assemble into fibers or form hydrogels due to the high hydrophilicity of HA. However, coassembly of <b>HA-BTA</b> with <b>BTA-OEG<sub>4</sub></b> resulted in the formation of long fibers, similar to those formed by <b>BTA-OEG<sub>4</sub></b> alone, and hydrogels were produced with tunable stiffness ranging from 250 to 700 Pa, which is 10-fold higher than that of hydrogels assembled with only <b>BTA-OEG<sub>4</sub></b>. Further coassembly of <b>BTA-OEG<sub>4</sub></b> fibers with other polysaccharides showed that except for dextran, all polysaccharides studied interacted with <b>BTA-OEG<sub>4</sub></b> fibers. The possibility of incorporating polysaccharides into BTA-based materials paves the way for the creation of dynamic complex biomaterials.
Project description:Supramolecular systems are intrinsically dynamic and sensitive to changes in molecular structure and external conditions. Because of these unique properties, strategies to control polymer length, composition, comonomer sequence, and morphology have to be developed for sufficient control over supramolecular copolymerizations. We designed photoresponsive, mono acyl hydrazone functionalized benzene-1,3,5-tricarboxamide (<b>m-BTA</b>) monomers that play a dual role in the coassembly with achiral alkyl BTAs (<b>a-BTA</b>). In the <i>E</i> isomer form, the chiral <b>m-BTA</b> monomers intercalate into stacks of <b>a-BTA</b> and dictate the chirality of the helices. Photoisomerization to the <i>Z</i> isomer transforms the intercalator into a chain capper, allowing dynamic shortening of chain length in the supramolecular aggregates. We combine optical spectroscopy and light-scattering experiments with theoretical modeling to show the reversible decrease in length when switching from the <i>E</i> to <i>Z</i> isomer of <b>m-BTA</b> in the copolymer with inert <b>a-BTA</b>. With a mass-balance thermodynamic model, we gain additional insights into the composition of copolymers and length distributions of the species over a broad range of concentrations and mixing ratios of <b>a-BTA</b>/<b>m-BTA</b>. Moreover, the model was used to predict the impact of an additive (chain capper and intercalator) on the chain length over a range of concentrations, showing a remarkable amplification of efficiency at high concentrations. By employing a stimuli-responsive comonomer in a mostly inert polymer, we can cooperatively amplify the effect of the switching and obtain photocontrol of polymer length. Moreover, this dynamic decrease in chain length causes a macroscopic gel-to-sol phase transformation of the copolymer gel, although 99.4% of the organogel is inert to the light stimulus.
Project description:The fast dynamics occurring in natural processes increases the difficulty of creating biomaterials capable of mimicking Nature. Within synthetic biomaterials, water-soluble supramolecular polymers show great potential in mimicking the dynamic behavior of these natural processes. In particular, benzene-1,3,5-tricaboxamide (BTA)-based supramolecular polymers have shown to be highly dynamic through the exchange of monomers within and between fibers, but their suitability as biomaterials has not been yet explored. Herein we systematically study the interactions of BTA supramolecular polymers bearing either tetraethylene glycol or mannose units at the periphery with different biological entities. When BTA fibers were incubated with bovine serum albumin (BSA), the protein conformation was only affected by the fibers containing tetraethylene glycol at the periphery (BTA-OEG4). Coarse-grained molecular simulations showed that BSA interacted with BTA-OEG4 fibers rather than with BTA-OEG4 monomers that are present in solution or that may exchange out of the fibers. Microscopy studies revealed that, in the presence of BSA, BTA-OEG4 retained their fiber conformation although their length was slightly shortened. When further incubated with fetal bovine serum (FBS), both long and short fibers were visualized in solution. Nevertheless, in the hydrogel state, the rheological properties were remarkably preserved. Further studies on the cellular compatibility of all the BTA assemblies and mixtures thereof were performed in four different cell lines. A low cytotoxic effect at most concentrations was observed, confirming the suitability of utilizing functional BTA supramolecular polymers as dynamic biomaterials.
Project description:The development and in-depth analysis of T4 DNA ligase-catalyzed DNA templated oligonucleotide polymerization toward the generation of diversely functionalized nucleic acid polymers is described. The NNNNT codon set enables low codon bias, high fidelity, and high efficiency for the polymerization of ANNNN libraries comprising various functional groups. The robustness of the method was highlighted in the copolymerization of a 256-membered ANNNN library comprising 16 sub-libraries modified with different functional groups. This enabled the generation of diversely functionalized synthetic nucleic acid polymer libraries with 93.8?% fidelity. This process should find ready application in DNA nanotechnology, DNA computing, and in?vitro evolution of functional nucleic acid polymers.
Project description:Multivalency has an important but poorly understood role in molecular self-organization. We present the noncovalent synthesis of a multicomponent supramolecular polymer in which chemically distinct monomers spontaneously coassemble into a dynamic, functional structure. We show that a multivalent recruiter is able to bind selectively to one subset of monomers (receptors) and trigger their clustering along the self-assembled polymer, behavior that mimics raft formation in cell membranes. This phenomenon is reversible and affords spatiotemporal control over the monomer distribution inside the supramolecular polymer by superselective binding of single-strand DNA to positively charged receptors. Our findings reveal the pivotal role of multivalency in enabling structural order and nonlinear recognition in water-soluble supramolecular polymers, and it offers a design principle for functional, structurally defined supramolecular architectures.