Constitutional Dynamic Networks Research Articles

Enzyme-Guided Selection and Cascaded Emergence of Nanostructured Constitutional Dynamic Networks.

Enzymes (endonucleases) are coupled to constitutional dynamic networks to stimulate the selection of a constituent and cascaded emergence of a new network. This is exemplified with the EcoRI-dictated depletion of a network and selection of a constituent that activates the cascaded emergence of a new network. The new network is further depleted by HindIII to a selected constituent that can be coupled to the cascaded emergence of a dynamic network. In addition, upon subjecting a [3 × 3] constitutional dynamic network to endonucleases EcoRI and HindIII, the programmed hierarchical selection of [2 × 2] constitutional dynamic networks followed by the biocatalytic selection of a constituent for the subsequent emergence of new networks is demonstrated.

Triple Self-Sorting in Constitutional Dynamic Networks: Parallel Generation of Imine-Based CuI , FeII , and ZnII Complexes.

Three imine‐based metal complexes, having no overlap in terms of their compositions, have been simultaneously generated from the self‐sorting of a constitutional dynamic library (CDL) containing three amines, three aldehydes, and three metal salts. The hierarchical ordering of the stability of the three metal complexes assembled and the leveraging of the antagonistic and agonistic relationships existing between the constituents within the constitutional dynamic network corresponding to the CDL were pivotal in achieving the sorting. Examination of the process by NMR spectroscopy showed that the self‐sorting of the FeII and ZnII complexes depended on an interplay between the thermodynamic driving forces and a kinetic trap involved in their assembly. These results also exemplify the concept of “simplexity”—the fact that the output of a self‐assembling system may be simplified by increasing its initial compositional complexity—as the two complexes could self‐sort only in the presence of the third pair of organic components, those of the CuI complex.

Triple Self‐Sorting in Constitutional Dynamic Networks: Parallel Generation of Imine‐Based CuI, FeII, and ZnII Complexes

AbstractThree imine‐based metal complexes, having no overlap in terms of their compositions, have been simultaneously generated from the self‐sorting of a constitutional dynamic library (CDL) containing three amines, three aldehydes, and three metal salts. The hierarchical ordering of the stability of the three metal complexes assembled and the leveraging of the antagonistic and agonistic relationships existing between the constituents within the constitutional dynamic network corresponding to the CDL were pivotal in achieving the sorting. Examination of the process by NMR spectroscopy showed that the self‐sorting of the FeII and ZnII complexes depended on an interplay between the thermodynamic driving forces and a kinetic trap involved in their assembly. These results also exemplify the concept of “simplexity”—the fact that the output of a self‐assembling system may be simplified by increasing its initial compositional complexity—as the two complexes could self‐sort only in the presence of the third pair of organic components, those of the CuI complex.

MicroRNA-Guided Selective Release of Loads from Micro-/Nanocarriers Using Auxiliary Constitutional Dynamic Networks.

Two different drug micro-carriers consisting of doxorubicin-dextran (DOX-D)- and camptothecin-modified carboxymethyl cellulose (CPT-CMC)-loaded nucleic acid-stabilized microcapsules, MC-1 and MC-2, or two different nanocarriers consisting of nucleic-acid-locked doxorubicin (DOX)- and camptothecin (CPT)-loaded metal–organic framework nanoparticles, NMOF-1 and NMOF-2, are coupled to auxiliary constitutional dynamic networks, CDNs, for the triggered release of the drugs. CDN “S” composed of four constituents AA′’, AB′, BA′, and BB′, and two hairpin structures, H1 and H2, leads to the CDN “S”-guided unlocking of the MC-1/MC-2 carriers and the release of DOX-D and CPT-CMC or of the NMOF-1 and NMOF-2 carriers that release DOX and CPT, respectively. The unlocking processes are activated by the cleavage of H1 and H2 by BB′ and BA′, respectively, to yield fragmented strands that unlock the gating units of the microcapsules/NMOFs carriers. In the presence of miRNA-155 or miRNA-124, dictated orthogonal reconfiguration of CDN “S” into CDN “X” or “Y” proceeds. The miRNA-155 stimulates the reconfiguration of CDN “S” to CDN “X”, where AA′ and BB′ are upregulated, and AB′ and BA′ are downregulated, leading to the enhanced release of DOX-D or DOX from the microcapsule/NMOFs carriers, and to the concomitant inhibition of the release of CPT-CMC or CPT from the respective carriers. Similarly, the miRNA-124-triggered reconfiguration of CDN “S” to CDN “Y” results in the BA′-guided cleavage of H2 and the preferred release of CPT-CMC or CPT from the respective carriers. The miRNA-triggered CDN-driven unlocking of the carriers stimulates the amplified and selective release of the drugs from the microcapsules/NMOFs carriers.

Self-sorting of two imine-based metal complexes: balancing kinetics and thermodynamics in constitutional dynamic networks.

A major hurdle in the development of complex constitutional dynamic networks (CDNs) is the lack of strategies to simultaneously control the output of two (or more) interconnected dynamic processes over several species, namely reversible covalent imine bond formation and dynamic metal–ligand coordination. We have studied in detail the self-sorting process of 11 constitutional dynamic libraries containing two different amines, aldehydes and metal salts into two imine-based metal complexes, having no overlap in terms of their compositions. This study allowed us to determine the factors influencing the fidelity of this process (concentration, electronic and steric parameters of the organic components, and nature of the metal cations). In all 11 systems, the outcome of the process was primarily determined by the ability of the octahedral metal ion to select its pair of components from the initial pool of components, with the composition of the weaker tetrahedral complex being imposed by the components rejected by the octahedral metal ions. Different octahedral metal ions required different levels of precision in the “assembling instructions” provided by the organic components of the CDN to guide it towards a sorted output. The concentration of the reaction mixture, and the electronic and steric properties of the initial components of the library were all found to influence the lifetime of unwanted metastable intermediates formed during the assembling of the two complexes.

A supramolecular aggregation-based constitutional dynamic network for information processing.

Concepts and strategies offered by constitutional dynamic chemistry (CDC) hold great promise for designing molecular computing systems adaptive to external environments. Despite demonstrable success in storing and processing chemical information using CDC, further employment of such constitutional dynamic networks (CDNs) for processing more complex digital information has not been realized yet. Herein, we introduced a supramolecular CDN based on the aggregation of cyanine MTC (Agg-CDN), which is composed of four reversibly interconvertible constituents, i.e. monomers, dimers, J-aggregates, and H-aggregates. We demonstrated that the equilibrated Agg-CDN is reconfigurable through constituent exchange in response to well-defined chemical inputs. More importantly, the equilibrated states of the Agg-CDN are spectroscopically distinguishable because of the unique optical properties of MTC. We further tuned the Agg-CDN to at least nine unique states for transforming the chemical inputs into digital outputs, and successfully employed it for encoding and encrypting complex digital information, such as multi-pixel images.

Time-Dependent Switching of Constitutional Dynamic Libraries and Networks from Kinetic to Thermodynamic Distributions.

The distribution of the constituents of a constitutional dynamic library (CDL) may undergo time-dependent changes as a function of the kinetics of the processes generating the CDL from its components. Thus, the constitutional dynamic network (CDN) representing the connections between the constituents changes from a kinetic distribution to the thermodynamic one as a function of time. We investigated the behavior of dynamic covalent libraries (DCLs) of four constituents generated by reversible formation of C═N bonds between four components, 2 aldehydes and 2 amino compounds, both in absence and in the presence of metal cations. The associated [2 × 2] networks underwent time-dependent changes from the initial kinetic distribution to the final thermodynamic one, involving an orthogonal switch from one diagonal to the other diagonal of the square [2 × 2] network leading to a very large change in distribution. The DCL constituents could be switched from kinetic products (imines) to thermodynamic products (oximes or acylhydrazones) based on the reactivities of the components and the thermodynamic stabilities of the constituents without addition of any external effector, solely on the basis of the intrinsic properties of the self-contained system. Such processes were achieved for purely organic DCLs/CDNs as well as for inorganic ones containing two metal cations, the latter changing from the silver(I) complex of an imine (kinetic product) to the zinc(II) complex of a hydrazone (thermodynamic product). The results bear relationship to out-of-equilibrium systems concerning kinetic behavior in adaptive chemistry.

Stiffness-switchable DNA-based constitutional dynamic network hydrogels for self-healing and matrix-guided controlled chemical processes

Constitutional dynamic networks (CDNs) attract interest as signal-triggered reconfigurable systems mimicking natural networks. The application of CDNs to control material properties is, however, a major challenge. Here we report on the design of a CDN consisting of four toehold-modified constituents, two of which act as bidentate units for chain-elongating, while the other two form a tetradentate structure acting as a crosslinking unit. Their hybridization yields a hydrogel of medium stiffness controlled by the balance between bidentate and tetradentate units. Stabilization of the tetradentate constituent by an auxiliary effector up-regulates the crosslinking unit, yielding a high-stiffness hydrogel. Conversely, stabilization of one of the bidentate constituents by an orthogonal effector enriches the chain-elongation units leading to a low-stiffness hydrogel. Using appropriate counter effectors, the hydrogels are reversibly switched across low-, medium- and high-stiffness states. The hydrogels are used to develop self-healing and controlled drug-release matrices and functional materials for operating biocatalytic cascades.

Triggered Interconversion of Dynamic Networks Composed of DNA-Tetrahedra Nanostructures.

Constitutional dynamic networks (CDNs) consisting of DNA tetrahedra allow the dynamically triggered adaptive control over the compositions and structures of the constituents. In one system, a CDN consisting of four tetrahedra constituents is orthogonally triggered by two alternative triggers, T1 or T2, to reconfigure into two different CDNs, revealing adaptive control-over the tetrahedra compositions in the two CDNs. In the presence of the counter triggers T1' or T2', the parent CDN is regenerated. In the second system, the assembly of a CDN consisting of four dimeric tetrahedra exhibiting variable sizes and shapes is described. The orthogonal triggering of the CDN by two different triggers T3 or T4, leads to the adaptive reconfiguration of the CDN into new equilibrated CDNs exhibiting control-over the compositions and shapes of the dimeric tetrahedra comprising the CDNs. Mg2+-ion-dependent DNAzyme units conjugated to the tetrahedra nanostructures and complementary electrophoretic experiments provide means to quantitatively evaluate the compositions of the different CDN systems. By the functionalization of the four-tetrahedra-based CDN system with two fluorophor donor-acceptor pairs and the orthogonal reconfiguration of the CDN in the presence of two alternative triggers, the control-over the FRET functions of the CDN systems is demonstrated.

Three-Dimensional Nucleic-Acid-Based Constitutional Dynamic Networks: Enhancing Diversity through Complexity of the Systems.

Inspired by nature, where gene regulatory networks consisting of intercommunicating constituents, each composed of three or more components, play a central role in the development of living systems, we use the information encoded in the base sequences of nucleic acids to construct three-dimensional constitutional dynamic networks (3D CDNs) consisting of eight three-component constituents (AiBjCk). Upon subjecting the parent 3D CDN I to four auxiliary nucleic acid triggers (T1, T2, T3, or T4), the adaptive reconfiguration of CDN I into four different CDNs (II, III, IV, or V) is demonstrated, and by applying two consecutive triggers or counter triggers, the adaptive reversible hierarchical control over the compositions of new CDN systems (VI, VII, VIII, or IX) is demonstrated. The labeling of the constituents with nine different Mg2+-ion-dependent DNAzyme reporter units and the incorporation of a fluorescent dye/anticocaine aptamer complex into the structure of one of the constituents enable the quantitative evaluation of the contents of the constituents in the different CDNs. The quantification of the compositions of the CDNs is based on the activities of the DNAzymes conjugated to the constituents, the fluorescence signals upon the cocaine-induced separation of the dye/aptamer complex, appropriate calibration curves, and the set of equations. These assessments are further supported by quantitative electrophoretic experiments of the respective CDNs.

Pattern Generation and Information Transfer through a Liquid/Liquid Interface in 3D Constitutional Dynamic Networks of Imine Ligands in Response to Metal Cation Effectors.

The immense discriminative capacity of the human olfactory chemosensory systems relies on the generation of a combinatorial signal in response to the interaction of a particular odorant molecule with many different olfactory receptors. In this work, we report the generation of distributional signals by the action of particular effectors, here metal cations, on dynamic covalent libraries (DCLs) of receptor molecules, here ligands for metal cations. Different effectors are discriminated by the formation of different constitutional distributions, which result from the adaptation of the DCL to the action of a particular cation effector through the selection and exchange of components. Compartmentalization by operation in a system of immiscible solvents (here water and chloroform) results in a 3D constitutional dynamic network (CDN), effecting distributional signal and information transfer between two domains, through the interface from the "writing" input phase (the IN-phase) and the "reading" output phase (the OUT-phase). Here, it is not the selectivity of a specific recognition process between a particular DCL member and a given effector that is key to the information processing, but the change in the distribution of the components and constituents, a dynamic pattern or fingerprint, induced in one phase in response to interaction with a given effector binding and transmitted to the other phase by component and constituent exchange across the phase boundary. Finally, the pattern recognition techniques such as hierarchical cluster analysis (HCA) and principal component analysis (PCA) were successfully applied to analyze the output generated by the action of different effectors on the higher order [5 × 5] DCL. Discrimination between different effectors was characterized by specific domains. Such data processing also opens the way toward extension to much larger DCLs.

Evolution of Nucleic‐Acid‐Based Constitutional Dynamic Networks Revealing Adaptive and Emergent Functions

AbstractThe evolution of networks is a fundamental unresolved issue in developing the area of systems chemistry. We introduce a versatile rewiring mechanism that leads to the emergence of nucleic‐acid‐based constitutional dynamic networks (CDNs). A two‐component constituent AA′ functionalized with a Mg2+‐ion‐dependent DNAzyme activator unit forms a complex with an intact hairpin HBB′ composed of B and B′ sequences. Cleavage of HBB′ leads to the two‐component constituent BB′, and its rewiring with AA′ yields CDN X composed of the equilibrated constituents AA′, AB′, BA′, and BB′. In analogy, subjecting AA′ to an intact hairpin HCC′ leads to the formation of CDN Y consisting of AA′, AC′, CA′, and CC′. Subjecting AA′ to the mixture of HBB′ and HCC′ evolves the [3×3] CDN Z, composed of nine constituents, thus demonstrating hierarchical adaptive properties. Furthermore, the DNAzyme units associated with the constituents are applied to tailor emerging catalytic functions from the different CDNs.

Evolution of Nucleic-Acid-Based Constitutional Dynamic Networks Revealing Adaptive and Emergent Functions.

The evolution of networks is a fundamental unresolved issue in developing the area of systems chemistry. We introduce a versatile rewiring mechanism that leads to the emergence of nucleic-acid-based constitutional dynamic networks (CDNs). A two-component constituent AA' functionalized with a Mg2+ -ion-dependent DNAzyme activator unit forms a complex with an intact hairpin HBB' composed of B and B' sequences. Cleavage of HBB' leads to the two-component constituent BB', and its rewiring with AA' yields CDN X composed of the equilibrated constituents AA', AB', BA', and BB'. In analogy, subjecting AA' to an intact hairpin HCC' leads to the formation of CDN Y consisting of AA', AC', CA', and CC'. Subjecting AA' to the mixture of HBB' and HCC' evolves the [3×3] CDN Z, composed of nine constituents, thus demonstrating hierarchical adaptive properties. Furthermore, the DNAzyme units associated with the constituents are applied to tailor emerging catalytic functions from the different CDNs.

Triggered reversible substitution of adaptive constitutional dynamic networks dictates programmed catalytic functions.

The triggered substitution of networks and their resulting functions play an important mechanism in biological transformations, such as intracellular metabolic pathways and cell differentiation. We describe the triggered, cyclic, reversible intersubstitution of three nucleic acid-based constitutional dynamic networks (CDNs) and the programmed catalytic functions guided by the interconverting CDNs. The transitions between the CDNs are activated by nucleic acid strand displacement processes acting as triggers and counter triggers, leading to the adaptive substitution of the constituents and to emerging catalytic functions dictated by the compositions of the different networks. The quantitative evaluation of the compositions of the different CDNs is achieved by DNAzyme reporters and complementary electrophoresis experiments. By coupling a library of six hairpins to the interconverting CDNs, the CDN-guided, emerging, programmed activities of three different biocatalysts are demonstrated. The study has important future applications in the development of sensor systems, finite-state logic devices, and selective switchable catalytic assemblies.

Consecutive feedback-driven constitutional dynamic networks

Cellular transformations are driven by environmentally triggered complex dynamic networks, which include signal-triggered feedback processes, cascaded reactions, and switchable transformations. We apply the structural and functional information encoded in the sequences of nucleic acids to construct signal-triggered constitutional dynamic networks (CDNs) that mimic the functions of natural networks. Using predesigned hairpin structures as triggers, the network generates functional strands, which stabilize one or the other of the constituents of the network, leading to feedback-driven reconfiguration and time-dependent equilibration of the networks. Using structurally designed hairpins, positive-feedback or negative-feedback mechanisms operated by the CDNs are demonstrated. With two predesigned hairpins, the coupled consecutive operations of negative/positive- or positive/positive- feedback cascades are accomplished. The time-dependent composition changes of the networks are well reproduced by chemical kinetics simulations that provide predictive behaviors of the network, under variable auxiliary conditions. Beyond mimicking natural network properties and functions by means of the synthetic nucleic-acid-based CDNs, the systems introduce versatile perspectives for the design of amplified sensors (sensing of miRNA-376a) and the development of logic gate circuits.

Multiple adaptation of constitutional dynamic networks and information storage in constitutional distributions of acylhydrazones.

We report a study of the behavior of four dynamic covalent libraries (DCLs) based on acylhydrazones aAbB and of the corresponding square constitutional dynamic networks (CDNs) NA-ND under the effect of three agents, namely, metal cations, base + metal cations and light irradiation; in particular, the successful switching of the CDN NB between two orthogonal distributions results, respectively, from metallo-selection and photo-selection. The four DCLs undergo triple adaptation when subjected to the three agents with the generation of specific CDN distributions characteristic of each of the four DCLs. The ternary outputs displayed by the DCLs present three states (-1, 0 and 1) related to three different constitutional distributions expressed in response to the triple inputs applied. This latter process amounts to the storage of molecular information in dynamic distributions rather than in selective interactions between complementary entities undergoing molecular recognition.

Controlling the Catalytic and Optical Properties of Aggregated Nanoparticles or Semiconductor Quantum Dots Using DNA-Based Constitutional Dynamic Networks.

Nucleic acid-based constitutional dynamic networks (CDNs) attract growing interest as a means to mimic complex biological networks. The triggered stabilization of the CDNs allows the dictated guided reversible reconfiguration and re-equilibration of the CDNs to other CDN configurations, where some of the constituents are up-regulated, while other constituents are down-regulated. Although substantial progress in controlling the adaptive dynamic control of the compositions of networks by means of auxiliary triggers was demonstrated, the use of CDNs as active ensembles for controlling chemical functionalities is still a challenge. We report on the assembly of signal-triggered CDN systems that guide the switchable aggregation of Au nanoparticles (NPs), thereby controlling their plasmonic properties and their catalytic functions (Au NPs-catalyzed oxidation of l-DOPA to dopachrome). In addition, we demonstrate that the triggered and orthogonal up-regulation and down-regulation of the constituents of the CDNs leads to the dictated aggregation of different-sized CdSe/ZnS quantum dots (QDs), cross-linked by K+-ion-stabilized G-quadruplex units. The incorporation of hemin into the G-quadruplex cross-linking units yields horseradish peroxidase-mimicking DNAzyme units that catalyze the generation of chemiluminescence via the oxidation of luminol by H2O2. The resulting chemiluminescence stimulates the chemiluminescence resonance energy transfer (CRET) process to the QDs, resulting in the luminescence of the two-sized QDs. By the application of appropriate triggers, the CDN-dictated up-regulation and down-regulation of the different-sized QDs aggregates are demonstrated, and the control over the photophysical functions of the different-sized QDs, by means of the CDNs, is highlighted.

DNA-Based Multiconstituent Dynamic Networks: Hierarchical Adaptive Control over the Composition and Cooperative Catalytic Functions of the Systems.

The information encoded in the base sequences of nucleic acids is used to construct [3 × 2] or [3 × 3] constitutional dynamic networks (CDNs) composed of six or nine constituents, respectively. In the presence of appropriate triggers, the adaptive and hierarchical reconfiguration of the CDNs is demonstrated. The reconfiguration of the CDNs, which involves the triggered stabilization and upregulation of a specific constituent is accompanied by the upregulation of the constituents that do not share component connectivities with the trigger-stabilized constituent, and by the concomitant downregulation of the constituents sharing component connectivities with the trigger-stabilized constituent. Using a set of different triggers, a series of reconfigured networks-in-networks are demonstrated. The operation and reconfiguration of the CDNs are based on the following motives: (i) Each of the constituents in the [3 × 2] or [3 × 3] CDNs is composed of a supramolecular structure consisting of two duplex-bridged double-loop quasi-circle units. The hybridization of a single-stranded trigger with the double-loop domain stabilizes the respective constituent, and this results in the reconfiguration of the CDNs. (ii) To each of the constituents is conjugated a Mg2+-ion-dependent DNAzyme that cleaves a sequence-specific fluorophore/quencher substrate. The time-dependent fluorescence changes upon the cleavage of the different substrates by the reporter DNAzymes, and the use of appropriate calibration curves, provide means to quantitativelyevaluate the contents of all constituents in the different CDNs. The triggered transitions of the parent [3 × 2] or [3 × 3] CDNs into three different CDNs using three different triggers, respectively, are exemplified. In addition, the transitions of the parent [3 × 2] or [3 × 3] CDNs using sequential triggers are demonstrated. Adaptive equilibrated reconfiguration of the CDNs subjected to triggers is demonstrated, and hierarchical adaptive dynamic transitions of the CDNs, subjected to two sequential triggering signals are highlighted. In addition, emerging catalytic functions driven by the adaptive and hierarchical transitions across different equilibrated states of the [3 × 3] CDNs are demonstrated.

Intercommunication of DNA-Based Constitutional Dynamic Networks.

Intercommunication between dynamic chemical networks plays a major role in cellular transformations. Inspired by nature, we introduce the intercommunication between two constitutional dynamic networks, CDNs, "S" and "T" composed, each, of four equilibrated supramolecular constituents AA', AB', BA', and BB', and of CC', CD', DC', and DD', respectively. Each of the constituents is conjugated to a Mg2+-ion-dependent DNAzyme unit that acts as a reporter element for the concentration of the respective constituent via the catalyzed cleavage of the fluorophore/quencher-functionalized substrate associated with the respective DNAzyme reporter. Also, constituents BB' (in CDN "S") and CC' (in CDN "T") include Mg2+-ion-dependent DNAzymes acting as activator units for generating triggering signals between the networks. Subjecting CDNs "S" and "T" to the catalytically cleavable hairpin trigger Hdd' or Haa', respectively, yields input strands that intercommunicate the CDNs by affecting the time-dependent re-equilibration of the constituents of the counter CDN without affecting the dynamic equilibrium of the constituents of the CDN that generates the triggering strands. Treatment of CDNs "S" and "T" with hairpins Hdd' and Haa' (or Hba'), respectively, stimulates autonomous positive/positive or positive/negative feedback to the programmed time-dependent up-regulation or down-regulation of the equilibrated constituents in the two CDNs.

Light‐Induced Reversible Reconfiguration of DNA‐Based Constitutional Dynamic Networks: Application to Switchable Catalysis

AbstractThe light‐induced reversible and cyclic reconfiguration of constitutional dynamic networks, consisting of supramolecular nucleic acid structures as constituents and a photoisomerizable trans/cis‐azobenzene‐functionalized nucleic acid as the trigger is demonstrated. In addition, the cyclic photochemical reconfiguration of the constitutional dynamic networks guides the switchable on/off operation of an emerging hemin/G‐quadruplex DNAzyme.