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Recent efforts in synthetic biology have shown the possibility of engineering distributed functions in populations of living cells, which requires the development of highly orthogonal, genetically encoded communication pathways. Cell-free transcription-translation (TXTL) reactions encapsulated in microcompartments enable prototyping of molecular communication channels and their integration into engineered genetic circuits by mimicking critical cell features, such as gene expression, cell size, and cell individuality within a community. In this review, we discuss the uses of cell-free transcription-translation reactions for the development of synthetic genetic circuits, with a special focus on the use of microcompartments supporting this reaction. We highlight several studies where molecular communication between non-living microcompartments and living cells have been successfully engineered., (Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.)

DNA-based molecular circuits allow autonomous signal processing, but their actuation has relied mostly on RNA/DNA-based inputs, limiting their application in synthetic biology, biomedicine and molecular diagnostics. Here we introduce a generic method to translate the presence of an antibody into a unique DNA strand, enabling the use of antibodies as specific inputs for DNA-based molecular computing. Our approach, antibody-templated strand exchange (ATSE), uses the characteristic bivalent architecture of antibodies to promote DNA-strand exchange reactions both thermodynamically and kinetically. Detailed characterization of the ATSE reaction allowed the establishment of a comprehensive model that describes the kinetics and thermodynamics of ATSE as a function of toehold length, antibody-epitope affinity and concentration. ATSE enables the introduction of complex signal processing in antibody-based diagnostics, as demonstrated here by constructing molecular circuits for multiplex antibody detection, integration of multiple antibody inputs using logic gates and actuation of enzymes and DNAzymes for signal amplification.

Scaffold proteins regulate cell signalling by promoting the proximity of putative interaction partners. Although they are frequently applied in cellular settings, fundamental understanding of them in terms of, amongst other factors, quantitative parameters has been lagging behind. Here we present a scaffold protein platform that is based on the native 14-3-3 dimeric protein and is controllable through the action of a small-molecule compound, thus permitting study in an in vitro setting and mathematical description. Robust small-molecule regulation of caspase-9 activity through induced dimerisation on the 14-3-3 scaffold was demonstrated. The individual parameters of this system were precisely determined and used to develop a mathematical model of the scaffolding concept. This model was used to elucidate the strong cooperativity of the enzyme activation mediated by the 14-3-3 scaffold. This work provides an entry point for the long-needed quantitative insights into scaffold protein functioning and paves the way for the optimal use of reengineered 14-3-3 proteins as chemically inducible scaffolds in synthetic systems., (© 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

Meditopes are cyclic peptides that bind in a specific pocket in the antigen-binding fragment of a therapeutic antibody such as cetuximab. Provided their moderate affinity can be enhanced, meditope peptides could be used as specific non-covalent and paratope-independent handles in targeted drug delivery, molecular imaging, and therapeutic drug monitoring. Here we show that the affinity of a recently reported meditope for cetuximab can be substantially enhanced using a combination of yeast display and deep mutational scanning. Deep sequencing was used to construct a fitness landscape of this protein-peptide interaction, and four mutations were identified that together improved the affinity for cetuximab 10-fold to 15 nm Importantly, the increased affinity translated into enhanced cetuximab-mediated recruitment to EGF receptor-overexpressing cancer cells. Although in silico Rosetta simulations correctly identified positions that were tolerant to mutation, modeling did not accurately predict the affinity-enhancing mutations. The experimental approach reported here should be generally applicable and could be used to develop meditope peptides with low nanomolar affinity for other therapeutic antibodies., (© 2017 by The American Society for Biochemistry and Molecular Biology, Inc.)

The modulation of the hierarchical nucleated self-assembly of tri-β(3) -peptides has been studied. β(3) -Tyrosine provided a handle to control the assembly process through host-guest interactions with CB[7] and CB[8]. By varying the cavity size from CB[7] to CB[8] distinct phases of assembling tri-β(3) -peptides were arrested. Given the limited size of the CB[7] cavity, only one aromatic β(3) -tyrosine can be simultaneously hosted and, hence, CB[7] was primarily acting as an inhibitor of self-assembly. In strong contrast, the larger CB[8] can form a ternary complex with two aromatic amino acids and hence CB[8] was acting primarily as cross-linker of multiple fibers and promoting the formation of larger aggregates. General insights on modulating supramolecular assembly can lead to new ways to introduce functionality in supramolecular polymers., (© 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

Supramolecular split-enzyme complementation restores enzymatic activity and allows for on-off switching. Split-luciferase fragment pairs were provided with an N-terminal FGG sequence and screened for complementation through host-guest binding to cucurbit[8]uril (Q8). Split-luciferase heterocomplex formation was induced in a Q8 concentration dependent manner, resulting in a 20-fold upregulation of luciferase activity. Supramolecular split-luciferase complementation was fully reversible, as revealed by using two types of Q8 inhibitors. Competition studies with the weak-binding FGG peptide revealed a 300-fold enhanced stability for the formation of the ternary heterocomplex compared to binding of two of the same fragments to Q8. Stochiometric binding by the potent inhibitor memantine could be used for repeated cycling of luciferase activation and deactivation in conjunction with Q8, providing a versatile module for in vitro supramolecular signaling networks., (© 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

The complexity of biomolecular systems inevitably leads to a degree of competition between the noncovalent interactions involved. However, the outcome of biological processes is generally very well-defined often due to the competition of these interactions. In contrast, specificity in synthetic supramolecular systems is usually based on the presence of a minimum set of alternative assembly pathways. While the latter might simplify the system, it prevents the selection of specific structures and thereby limits the adaptivity of the system. Therefore, artificial systems containing competing interactions are vital to stimulate the development of more adaptive and lifelike synthetic systems. Here, we present a detailed study on the self-assembly behavior of a C2v-symmetrical tritopic molecule, functionalized with three self-complementary ureidopyrimidinone (UPy) motifs. Due to a shorter linker connecting one of these UPys, two types of cycles with different stabilities can be formed, which subsequently dimerize intermolecularly via the third UPy. The UPy complementary 2,7-diamido-1,8-naphthyridine (NaPy) motif was gradually added to this mixture in order to examine its effect on the cycle distribution. As a result of the C2v-symmetry of the tritopic UPy, together with small differences in binding strength, the cycle ratio can be regulated by altering the concentration of NaPy. We show that this ratio can be increased to an extent where one type of cycle is formed almost exclusively.

The self-assembly of molecular building blocks into one-dimensional supramolecular architectures has opened up new frontiers in materials science. Due to the noncovalent interactions between the monomeric units, these architectures are intrinsically dynamic, and understanding their kinetic driving forces is key to rationally programming their morphology and function. To understand the self-assembly dynamics of supramolecular polymerizations (SP), kinetic models based on aggregate growth by sequential monomer association and dissociation have been analyzed. However, fragmentation and coagulation events can also play a role, as evident from studies on peptide self-assembly and the fact that aggregations can be sensitive to mechanical agitations. Here, we analyze how fragmentation and coagulation events influence SP kinetics by theoretical analysis of self-assembling systems of increasing complexity. Our analysis starts with single-component systems in which aggregates are able to grow via an isodesmic or cooperative nucleation-elongation mechanism. Subsequently, equilibration dynamics in cooperative two-component supramolecular copolymerizations are investigated. In the final part, we reveal how aggregate growth in the presence of competing, kinetically controlled pathways is influenced by fragmentation and coagulation reactions and reveal how seed-induced growth can give rise to block copolymers. Our analysis shows how fragmentation and coagulation reactions are able to modulate SP kinetics in ways that are highly system dependent.

Drop-based microfluidics have recently become a novel tool by providing a stable linkage between phenotype and genotype for high throughput screening. However, use of drop-based microfluidics for screening high-affinity peptide binders has not been demonstrated due to the lack of a sensitive functional assay that can detect single DNA molecules in drops. To address this sensitivity issue, we introduced in vitro two-hybrid system (IVT2H) into microfluidic drops and developed a streamlined mix-and-read drop-IVT2H method to screen a random DNA library. Drop-IVT2H was based on the correlation between the binding affinity of two interacting protein domains and transcriptional activation of a fluorescent reporter. A DNA library encoding potential peptide binders was encapsulated with IVT2H such that single DNA molecules were distributed in individual drops. We validated drop-IVT2H by screening a three-random-residue library derived from a high-affinity MDM2 inhibitor PMI. The current drop-IVT2H platform is ideally suited for affinity screening of small-to-medium-sized libraries (10(3)-10(6)). It can obtain hits within a single day while consuming minimal amounts of reagents. Drop-IVT2H simplifies and accelerates the drop-based microfluidics workflow for screening random DNA libraries, and represents a novel alternative method for protein engineering and in vitro directed protein evolution.

Living cells are able to produce a wide variety of biological responses when subjected to biochemical stimuli. It has become apparent that these biological responses are regulated by complex chemical reaction networks (CRNs). Unravelling the function of these circuits is a key topic of both systems biology and synthetic biology. Recent progress at the interface of chemistry and biology together with the realisation that current experimental tools are insufficient to quantitatively understand the molecular logic of pathways inside living cells has triggered renewed interest in the bottom-up development of CRNs. This builds upon earlier work of physical chemists who extensively studied inorganic CRNs and showed how a system of chemical reactions can give rise to complex spatiotemporal responses such as oscillations and pattern formation. Using purified biochemical components, in vitro synthetic biologists have started to engineer simplified model systems with the goal of mimicking biological responses of intracellular circuits. Emulation and reconstruction of system-level properties of intracellular networks using simplified circuits are able to reveal key design principles and molecular programs that underlie the biological function of interest. In this Tutorial Review, we present an accessible overview of this emerging field starting with key studies on inorganic CRNs followed by a discussion of recent work involving purified biochemical components. Finally, we review recent work showing the versatility of programmable biochemical reaction networks (BRNs) in analytical and diagnostic applications.

While the sensitive dependence of the functional characteristics of self-assembled nanofibers on the molecular structure of their building blocks is well-known, the crucial influence of the dynamics of the assembly process is often overlooked. For natural protein-based fibrils, various aggregation mechanisms have been demonstrated, from simple primary nucleation to secondary nucleation and off-pathway aggregation. Similar pathway complexity has recently been described in synthetic supramolecular polymers and has been shown to be intimately linked to their morphology. We outline a general method to investigate the consequences of the presence of multiple assembly pathways, and show how kinetic analysis can be used to distinguish different assembly mechanisms. We illustrate our combined experimental and theoretical approach by studying the aggregation of chiral bipyridine-extended 1,3,5-benzenetricarboxamides (BiPy-1) in n-butanol as a model system. Our workflow consists of nonlinear least-squares analysis of steady-state spectroscopic measurements, which cannot provide conclusive mechanistic information but yields the equilibrium constants of the self-assembly process as constraints for subsequent kinetic analysis. Furthermore, kinetic nucleation-elongation models based on one and two competing pathways are used to interpret time-dependent spectroscopic measurements acquired using stop-flow and temperature-jump methods. Thus, we reveal that the sharp transition observed in the aggregation process of BiPy-1 cannot be explained by a single cooperative pathway, but can be described by a competitive two-pathway mechanism. This work provides a general tool for analyzing supramolecular polymerizations and establishing energetic landscapes, leading to mechanistic insights that at first sight may seem unexpected and counterintuitive.

Living large: Rational design of self-assembly pathways has been demonstrated in supramolecular polymers. By controlling the concentration of an aggregation-competent monomer through intramolecular interactions, living supramolecular polymerization conditions were achieved. This universal approach can be used to obtain aggregates of well-defined length and narrow dispersity, and allows access to new supramolecular polymer architectures., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Molecular programming allows for the bottom-up engineering of biochemical reaction networks in a controlled in vitro setting. These engineered biochemical reaction networks yield important insight in the design principles of biological systems and can potentially enrich molecular diagnostic systems. The DNA polymerase-nickase-exonuclease (PEN) toolbox has recently been used to program oscillatory and bistable biochemical networks using a minimal number of components. Previous work has reported the automatic construction of in silico descriptions of biochemical networks derived from the PEN toolbox, paving the way for generating networks of arbitrary size and complexity in vitro. Here, we report an automated approach that further bridges the gap between an in silico description and in vitro realization. A biochemical network of arbitrary complexity can be globally screened for parameter values that display the desired function and combining this approach with robustness analysis further increases the chance of successful in vitro implementation. Moreover, we present an automated design procedure for generating optimal DNA sequences, exhibiting key characteristics deduced from the in silico analysis. Our in silico method has been tested on a previously reported network, the Oligator, and has also been applied to the design of a reaction network capable of displaying adaptation in one of its components. Finally, we experimentally characterize unproductive sequestration of the exonuclease to phosphorothioate protected ssDNA strands. The strong nonlinearities in the degradation of active components caused by this unintended cross-coupling are shown computationally to have a positive effect on adaptation quality.

Recently, we reported an organocatalytic system in which buffering of the molecular catalyst by supramolecular interactions results in a robust system displaying concentration-independent catalytic activity. Here, we demonstrate the design principles of the supramolecular buffering by ring-chain competition using a combined experimental and theoretical approach. Our analysis shows that supramolecular buffering of a molecule is caused by its participation as a chain stopper in supramolecular ring-chain equilibria, and we reveal here the influence of various thermodynamic parameters. Model predictions based on independently measured equilibrium constants corroborate experimental data of several molecular systems in which buffering occurs via competition between cyclization, growth of linear chains, and end-capping by the chain-stopper. Our analysis reveals that the effective molarity is the critical parameter in optimizing the broadness of the concentration regime in which supramolecular ring-chain buffering occurs as well as the maximum concentration of the buffered molecule. To conclude, a side-by-side comparison of supramolecular ring-chain buffering, pH buffering, and molecular titration is presented.

Life is sustained by complex systems operating far from equilibrium and consisting of a multitude of enzymatic reaction networks. The operating principles of biology's regulatory networks are known, but the in vitro assembly of out-of-equilibrium enzymatic reaction networks has proved challenging, limiting the development of synthetic systems showing autonomous behaviour. Here, we present a strategy for the rational design of programmable functional reaction networks that exhibit dynamic behaviour. We demonstrate that a network built around autoactivation and delayed negative feedback of the enzyme trypsin is capable of producing sustained oscillating concentrations of active trypsin for over 65 h. Other functions, such as amplification, analog-to-digital conversion and periodic control over equilibrium systems, are obtained by linking multiple network modules in microfluidic flow reactors. The methodology developed here provides a general framework to construct dissipative, tunable and robust (bio)chemical reaction networks.

A wet stamping method to precisely control concentrations of enzymes and inhibitors in place and time inside layered gels is reported. By combining enzymatic reactions such as autocatalysis and inhibition with spatial delivery of components through soft lithographic techniques, a biochemical reaction network capable of recognizing the spatial distribution of an enzyme was constructed. The experimental method can be used to assess fundamental principles of spatiotemporal order formation in chemical reaction networks., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Sequence control in supramolecular copolymers is limited by the selectivity of the associating monomer end groups. Here we introduce the use of monomers with aminopyrimidinone and aminohydroxynaphthyridine quadruple hydrogen bonding end groups, which both homodimerize, but form even stronger heterodimers. These features allow the formation of supramolecular copolymers with a tunable composition and a preference for alternating sequences.

The multidrug transporters breast cancer resistance protein (BCRP), multidrug-resistance protein 1 (MDR1), and multidrug-resistance-associated protein (MRP) 2 and 3 eliminate toxic compounds from tissues and the body and affect the pharmacokinetics of many drugs and other potentially toxic compounds. The food-derived carcinogen PhIP (2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine) is transported by BCRP, MDR1, and MRP2. To investigate the overlapping functions of Bcrp1, Mdr1a/b, and Mrp2 in vivo, we generated Bcrp1;Mdr1a/b;Mrp2(-/-) mice, which are viable and fertile. These mice, together with Bcrp1;Mrp2;Mrp3(-/-) mice, were used to study the effects of the multidrug transporters on the pharmacokinetics of PhIP and its metabolites. Thirty minutes after oral or intravenous administration of PhIP (1 mg/kg), the PhIP levels in the small intestine were reduced 4- to 6-fold in Bcrp1;Mdr1a/b;Mrp2(-/) (-) and Bcrp1;Mrp2;Mrp3(-/-) mice compared with wild-type mice. Fecal excretion of PhIP was reduced 8- to 20-fold in knockouts. Biliary PhIP excretion was reduced 41-fold in Bcrp1;Mdr1a/b;Mrp2(-/-) mice. Biliary and small intestine levels of PhIP metabolites were reduced in Bcrp1;Mrp2-deficient mice. Furthermore, in both knockout strains, kidney levels and urinary excretion of genotoxic PhIP-metabolites were significantly increased, suggesting that reduced biliary excretion of PhIP and PhIP metabolites leads to increased urinary excretion of these metabolites and increased systemic exposure. Bcrp1 and Mdr1a limited PhIP brain accumulation. In Bcrp1;Mrp2;Mrp3(-/-), but not Bcrp1;Mdr1a/b;Mrp(-/-) mice, the carcinogenic metabolites N2-OH-PhIP (2-hydroxyamino-1-methyl-6-phenylimidazo[4,5-b]pyridine) and PhIP-5-sulfate (a genotoxicity marker) accumulated in liver tissue, indicating that Mrp3 is involved in the sinusoidal secretion of these compounds. We conclude that Bcrp1, Mdr1a/b, Mrp2, and Mrp3 significantly affect tissue disposition and biliary and fecal elimination of PhIP and its carcinogenic metabolites and may affect PhIP-induced carcinogenesis as a result.

Here, we report an engineering approach toward multicomponent self-assembly processes by developing a methodology to circumvent spurious, metastable assemblies. The formation of metastable aggregates often hampers self-assembly of molecular building blocks into the desired nanostructures. Strategies are explored to master the pathway complexity and avoid off-pathway aggregates by optimizing the rate of assembly along the correct pathway. We study as a model system the coassembly of two monomers, the R- and S-chiral enantiomers of a π-conjugated oligo(p-phenylene vinylene) derivative. Coassembly kinetics are analyzed by developing a kinetic model, which reveals the initial assembly of metastable structures buffering free monomers and thereby slows the formation of thermodynamically stable assemblies. These metastable assemblies exert greater influence on the thermodynamically favored self-assembly pathway if the ratio between both monomers approaches 1:1, in agreement with experimental results. Moreover, competition by metastable assemblies is highly temperature dependent and hampers the assembly of equilibrium nanostructures most effectively at intermediate temperatures. We demonstrate that the rate of the assembly process may be optimized by tuning the cooling rate. Finally, it is shown by simulation that increasing the driving force for assembly stepwise by changing the solvent composition may circumvent metastable pathways and thereby force the assembly process directly into the correct pathway.

Delineating design principles of biological systems by reconstitution of purified components offers a platform to gauge the influence of critical physicochemical parameters on minimal biological systems of reduced complexity. Here we unravel the effect of strong reversible inhibitors on the spatiotemporal propagation of enzymatic reactions in a confined environment in vitro. We use micropatterned, enzyme-laden agarose gels which are stamped on polyacrylamide films containing immobilized substrates and reversible inhibitors. Quantitative fluorescence imaging combined with detailed numerical simulations of the reaction-diffusion process reveal that a shallow gradient of enzyme is converted into a steep product gradient by addition of strong inhibitors, consistent with a mathematical model of molecular titration. The results confirm that ultrasensitive and threshold effects at the molecular level can convert a graded input signal to a steep spatial response at macroscopic length scales., (Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Cooperative aggregation of monomers into one-dimensional nanostructures typically results in elongated objects. Here we analyse in depth the self-assembly of an N-monoarylated perylene bisimide which shows characteristics of a cooperative growth mechanism but unexpectedly yields objects of small size, due to anti-cooperativity by attenuated growth.

Estrogen receptor alpha (ERα) is involved in numerous physiological and pathological processes, including breast cancer. Breast cancer therapy is therefore currently directed at inhibiting the transcriptional potency of ERα, either by blocking estrogen production through aromatase inhibitors or antiestrogens that compete for hormone binding. Due to resistance, new treatment modalities are needed and as ERα dimerization is essential for its activity, interference with receptor dimerization offers a new opportunity to exploit in drug design. Here we describe a unique mechanism of how ERα dimerization is negatively controlled by interaction with 14-3-3 proteins at the extreme C terminus of the receptor. Moreover, the small-molecule fusicoccin (FC) stabilizes this ERα/14-3-3 interaction. Cocrystallization of the trimeric ERα/14-3-3/FC complex provides the structural basis for this stabilization and shows the importance of phosphorylation of the penultimate Threonine (ERα-T(594)) for high-affinity interaction. We confirm that T(594) is a distinct ERα phosphorylation site in the breast cancer cell line MCF-7 using a phospho-T(594)-specific antibody and by mass spectrometry. In line with its ERα/14-3-3 interaction stabilizing effect, fusicoccin reduces the estradiol-stimulated ERα dimerization, inhibits ERα/chromatin interactions and downstream gene expression, resulting in decreased cell proliferation. Herewith, a unique functional phosphosite and an alternative regulation mechanism of ERα are provided, together with a small molecule that selectively targets this ERα/14-3-3 interface.

Evaporative self-assembly of dilute solutions containing single-chain polymeric nanoparticles results in characteristic morphologies imaged using atomic force microscopy. Quantitative comparison of experimental data to morphologies obtained by lattice-gas simulations shows that the nonequilibrium patterns emerge from a complex interplay between dewetting, solvent evaporation and nanoparticle diffusion.

The interplay of two subsequent aggregation processes results in a symmetry-breaking phenomenon in an achiral self-assembling system. Partially fluorinated benzene-1,3,5-tricarboxamide molecules self-assemble into a racemic mixture of one-dimensional P- and M-helical aggregates, followed by bundling into optically active higher-order aggregates or fibers., (Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The molecular origin of the isotope-induced diastereomeric enrichment in helical supramolecular polymers consisting of trialkylbenzene-1,3,5-tricarboxamides (BTAs) is studied using plane-wave DFT calculations. We demonstrate that the creation of a chiral center at the α-position of the alkyl chains of a BTA by H-D exchange leads to a small but notable preference for the formation of supramolecular hydrogen bonded structures with a particular helicity. The bias for one helical sense preference is caused by the orientation of the vibrational eigenmodes of the C-H and C-D stretching frequencies at the chiral center and by hyperconjugative destabilization of the anti C-H orbital.

After their first synthesis in 1915 by Curtius, benzene-1,3,5-tricarboxamides (BTAs) have become increasingly important in a wide range of scientific disciplines. Their simple structure and wide accessibility in combination with a detailed understanding of their supramolecular self-assembly behaviour allow full utilization of this versatile, supramolecular building block in applications ranging from nanotechnology to polymer processing and biomedical applications. While the opportunities in the former cases are connected to the self-assembly of BTAs into one-dimensional, nanometer-sized rod like structures stabilised by threefold H-bonding, their multivalent nature drives applications in the biomedical field. This review summarises the different types of BTAs that appeared in the recent literature and the applications they have been evaluated in. Currently, the first commercial applications of BTAs are emerging. The adaptable nature of this multipurpose building block promises a bright future.

The influence of the ratio between poor and good solvent on the stability and dynamics of supramolecular polymers is studied via a combination of experiments and simulations. Step-wise addition of good solvent to supramolecular polymers assembled via a cooperative (nucleated) growth mechanism results in complete disassembly at a critical good/poor solvent ratio. In contrast, gradual disassembly profiles upon addition of good solvent are observed for isodesmic (non-nucleated) systems. Due to the weak association of good solvent molecules to monomers, the solvent-dependent aggregate stability can be described by a linear free-energy relationship. With respect to dynamics, the depolymerization of π-conjugated oligo(p-phenylene vinylene) (OPV) assemblies in methylcyclohexane (MCH) upon addition of chloroform as a good solvent is shown to proceed with a minimum rate around a critical chloroform/MCH solvent ratio. This minimum disassembly rate bears an intriguing resemblance to phenomena observed in protein unfolding, where minimum rates are observed at the thermodynamic midpoint of a protein denaturation experiment. A kinetic nucleation-elongation model in which the rate constants explicitly depend on the good solvent fraction is developed to rationalize the kinetic traces and further extend the insights by simulation. It is shown that cooperativity, i.e., the nucleation of new aggregates, plays a key role in the minimum polymerization and depolymerization rate at the critical solvent composition. Importantly, this shows that the mixing protocol by which one-dimensional aggregates are prepared via solution-based processing using good/poor solvent mixtures is of major influence on self-assembly dynamics.

We describe a model that rationalizes amplification of chirality in cooperative supramolecular copolymerization. The model extends nucleation-elongation based equilibrium models for growth of supramolecular homopolymers to the case of two monomer and aggregate types. Using the principle of mass-balance for the two monomer types, we derive a set of two nonlinear equations, describing the thermodynamic equilibrium state of the system. These equations can be solved by numerical methods, but also analytical approximations are derived. The equilibrium model allows two-sided growth of the aggregates and can be applied to symmetric supramolecular copolymerizations, corresponding to the situation in which the monomers are enantiomerically related, as well as to the more general case of nonsymmetric supramolecular copolymerizations. In detail, so-called majority-rules phenomena in supramolecular systems with isodesmic as well as cooperative growth are analyzed. Comparison of model predictions with experimental data shows that the model gives a very good description of both titration and melting curves. When the system shows cooperative growth, the model leads to a phase diagram in which the presence of the various aggregate types is given as a function of composition and temperature.

Self-assembly provides an attractive route to functional organic materials, with properties and hence performance depending sensitively on the organization of the molecular building blocks. Molecular organization is a direct consequence of the pathways involved in the supramolecular assembly process, which is more amenable to detailed study when using one-dimensional systems. In the case of protein fibrils, formation and growth have been attributed to complex aggregation pathways that go beyond traditional concepts of homogeneous and secondary nucleation events. The self-assembly of synthetic supramolecular polymers has also been studied and even modulated, but our quantitative understanding of the processes involved remains limited. Here we report time-resolved observations of the formation of supramolecular polymers from π-conjugated oligomers. Our kinetic experiments show the presence of a kinetically favoured metastable assembly that forms quickly but then transforms into the thermodynamically favoured form. Quantitative insight into the kinetic experiments was obtained from kinetic model calculations, which revealed two parallel and competing pathways leading to assemblies with opposite helicity. These insights prompt us to use a chiral tartaric acid as an auxiliary to change the thermodynamic preference of the assembly process. We find that we can force aggregation completely down the kinetically favoured pathway so that, on removal of the auxiliary, we obtain only metastable assemblies.

The understanding of multi-component mixtures of self-assembling molecules under thermodynamic equilibrium can only be advanced by a combined experimental and theoretical approach. In such systems, small differences in association energy between the various components can be significantly amplified at the supramolecular level via intricate nonlinear effects. Here we report a theoretical investigation of two-component, self-assembling systems in order to rationalize chiral amplification in cooperative supramolecular copolymerizations. Unlike previous models based on theories developed for covalent polymers, the models presented here take into account the equilibrium between the monomer pool and supramolecular polymers, and the cooperative growth of the latter. Using two distinct methodologies, that is, solving mass-balance equations and stochastic simulation, we show that monomer exchange accounts for numerous unexplained observations in chiral amplification in supramolecular copolymerization. In analogy with asymmetric catalysis, amplification of chirality in supramolecular polymers results in an asymmetric depletion of the enantiomerically related monomer pool.

The supramolecular oligomerization of three water-soluble C(3)-symmetrical discotic molecules is reported. The compounds all possess benzene-1,3,5-tricarboxamide cores and peripheral Gd(III)-DTPA (diethylene triamine pentaacetic acid) moieties, but differ in their linker units and thus in their propensity to undergo secondary interactions in H(2)O. The self-assembly behavior of these molecules was studied in solution using circular dichroism, UV/Vis spectroscopy, nuclear magnetic resonance, and cryogenic transmission electron microscopy. The aggregation concentration of these molecules depends on the number of secondary interactions and on the solvophobic character of the polymerizing moieties. Hydrophobic shielding of the hydrogen-bonding motif in the core of the discotic is of paramount importance for yielding stable, helical aggregates that are designed to be restricted in size through anti-cooperative, electrostatic, repulsive interactions., (Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Enzymes are a source of inspiration for chemists attempting to create versatile synthetic catalysts. In order to arrive at a polymeric chain carrying catalytic units separated spatially, it is a prerequisite to fold these polymers in water into well-defined compartmentalized architectures thus creating a catalytic core. Herein, we report the synthesis, physical properties, and catalytic activity of a water-soluble segmented terpolymer in which a helical structure in the apolar core is created around a ruthenium-based catalyst. The supramolecular chirality of this catalytic system is the result of the self-assembly of benzene-1,3,5-tricarboxamide side chains, while the catalyst arises from the sequential ruthenium-catalyzed living radical polymerization of the different monomers followed by ligand exchange. The polymers exhibit a two-state folding process and show transfer hydrogenation in water., (© 2011 American Chemical Society)

Understanding the molecular mechanism of cooperative self-assembly is a key component in the design of self-assembled supramolecular architectures across multiple length scales with defined function and composition. In this work, we use density functional theory to rationalize the experimentally observed cooperative growth of C(3)-symmetrical trialkylbenzene-1,3,5-tricarboxamide- (BTA-) based supramolecular polymers that self-assemble into ordered one-dimensional supramolecular structures through hydrogen bonding. Our analysis shows that the cooperative growth of these structures is caused by electrostatic interactions and nonadditive effects brought about by redistribution of the electron density with aggregate length.

A series of oligo(ethylene oxide) (oligoEO) substituted 2-ureido-pyrimidinones (UPy), differing in the number of ethylene oxide units and the length of the aliphatic spacer connecting the oligoEO side chain with the UPy group, have been prepared. It was found that variation in these structural parameters strongly influences the dimerization constant (K(dim)) of the UPy dimer and the association constant (K(a)) of UPy with 2,7-diamido-1,8-naphthyridine (NaPy) in chloroform. By analyzing the relation between dimerization strength, length of aliphatic spacer, and the number of EO units in the oligoEO chain, we present strong evidence that the reduction in hydrogen bond strength is caused by competitive intramolecular hydrogen bonding of the ether atoms of the oligoEO chain to the hydrogen bond donors of the UPy unit.

Ureido-pyrimidinone (UPy) dimers substituted with an additional urea functionality self-assemble into one-dimensional stacks in various solvents through lateral non-covalent interactions. (1)H NMR and DOSY studies in CDCl(3) suggest the formation of short stacks (<10), whereas temperature-dependent circular dichroism (CD) studies on chiral UPy dimers in heptane show the formation of much larger helical stacks. Analysis of the concentration-dependent evolution of chemical shift in CDCl(3) and the temperature-dependent CD effect in heptane suggest that this self-assembly process follows an isodesmic pathway in both solvents. The length of the aggregates is influenced by substituents attached to the urea functionality. In sharp contrast, UPy dimers carrying an additional urethane group do not self-assemble into ordered stacks, as is evident from the absence of a CD effect in heptane and the concentration-independent chemical shift of the alkylidene proton of the pyrimidinone ring in CDCl(3).

N-Centred benzene-1,3,5-tricarboxamides (N-BTAs) composed of chiral and achiral alkyl substituents were synthesised and their solid-state behaviour and self-assembly in dilute alkane solutions were investigated. A combination of differential scanning calorimetry (DSC), polarisation optical microscopy (POM) and X-ray diffraction revealed that the chiral N-BTA derivatives with branched 3,7-dimethyloctanoyl chains were liquid crystalline and the mesophase was assigned as Col(ho). In contrast, N-BTA derivatives with linear tetradecanoyl or octanoyl chains lacked a mesophase and were obtained as crystalline compounds. Variable-temperature infrared spectroscopy showed the presence of threefold, intermolecular hydrogen bonding between neighbouring molecules in the mesophase of the chiral N-BTAs. In the crystalline state at room temperature a more complicated packing between the molecules was observed. Ultraviolet and circular dichroism spectroscopy on dilute solutions of N-BTAs revealed a cooperative self-assembly behaviour of the N-BTA molecules into supramolecular polymers with preferred helicity when chiral alkyl chains were present. Both the sergeants-and-soldiers as well as the majority-rules principles were operative in stacks of N-BTAs. In fact, the self-assembly of N-BTAs resembles closely that of their carbonyl (C=O)-centred counterparts, with the exception that aggregation is weaker and amplification of chirality is less pronounced. The differences in the self-assembly of N- and C=O-BTAs were analysed by density functional theory (DFT) calculations. These reveal a substantially lower interaction energy between the monomeric units in the supramolecular polymers of N-BTAs. The lower interaction energy is due to the higher energy penalty for rotation around the Ph--NH bond compared to the Ph--CO bond and the diminished magnitude of dipole-dipole interactions. Finally, we observed that mixed stacks are formed in dilute solution when mixing N-BTAs and C=O BTAs.

To study the supramolecular polymerisation mechanisms of a self-assembling system, concentration- and temperature-dependent measurements can both be used to probe the transition from the molecular dissolved state to the aggregated state. In this report, both methods are evaluated to determine their effectiveness in identifying and quantifying the self-assembly mechanism for isodesmic and cooperative self-assembling systems. It was found that for a rapid and unambiguous determination of the self-assembly mechanism and its thermodynamic parameters, temperature-dependent measurements are more appropriate. These studies allow the acquisition of a large data set leading to an accurate determination of the self-assembly mechanism and quantification of the different thermodynamic parameters that describe the supramolecular polymerisation. For a comprehensive characterisation, additional concentration-dependent measurements can be performed.

We report on two diaminotriazine-equipped naphthalene derivatives that bind reversibly to a single-stranded DNA template or "tape-measure molecule" via hydrogen bonding, yielding monodisperse double-stranded DNA hybrids with one strand consisting of a supramolecular naphthalene backbone. These assemblies have been investigated extensively, both experimentally and theoretically. The structure and the templated self-assembly process of the complex have been characterized with UV-vis spectroscopy, circular dichroism spectroscopy, molecular dynamics simulations, cryo-transmission electron microscopy, liquid atomic force microscopy, electrospray ionization mass spectrometry, light scattering, and 1H NMR and infrared spectroscopy. We have found that the DNA hybrid complexes have a right-handed helical arrangement stabilized by pi-pi interactions and hydrogen bonds. The hydrophilic hydroxyl group at the end of the ethylene glycol of the guest molecule suppressed both the nontemplated self-assembly of the naphthalene guest molecules and the further aggregation of the entire DNA hybrid complex. Through the use of a theoretical mass-action model for the templated self-assembly, the host-guest and guest-guest interaction energies were estimated by fitting to the spectroscopic data. The differently estimated values of the interaction energies and thermodynamic parameters vary within experimental error, showing the self-consistency of the model. From the obtained correlation between the positions of the guest molecules bound on the template, we have obtained a qualitative theoretical picture of the way in which the guests are physically distributed on the templates. For short templates, the templates are filled one-by-one, even at moderate fractions of bound sites. For larger templates, the templates first have alternating sequences of filled and empty sections, after which, at large fractions of bound sites, virtually all of the binding sites for all template lengths are filled.

The supramolecular polymerization of two AB-type monomers capable of hydrogen-bond-mediated A x B heterocoupling and A x A homocoupling is discussed. The AB-type supramolecular polymerization is based on the strong interaction between self-dimerizing 2-ureido-pyrimidinone (UPy) and 2,7-diamido-1,8-naphthyridine (NaPy). In an effort to reduce the "self-stoppered" effect that is inherently present in these supramolecular polymerizations we used a novel ureido-pyrimidinone substituted with a dibutylamino group at the pyrimidinone ring. As a result of the substitution, the dimerization constant of the novel UPy unit is lowered compared to the previous UPy unit while the heterodimerization strength is retained. Unexpectedly, the increased selectivity toward heteroassociation not only influences the concentration-dependent degree of polymerization due to reduction of the "self-stoppered" effect but also has a pronounced effect on the ring-chain equilibrium by increasing the tendency to cyclize. In order to quantitatively explain our results, a model was developed that accurately predicts the degree of polymerization by taking into account homo- and heterodimerization as well as cyclization. Finally, molecular weight distributions for noncyclizing AB supramolecular polymerizations with and without a reversible A x A interaction are calculated. It is found that the molecular weight distribution becomes narrower when A x A interactions are present.

Substitution of hydrogen bond directed supramolecular assemblies with ethylene glycol chains leads to a reduction in the association constant in apolar solvents, where the reduction of the association constant is dependent on the length of the aliphatic spacer connecting the hydrogen bonds and the ethylene glycol chain.

The kinetics of association of ureido-pyrimidinone (U) dimers, present either in the 4[1H]-keto form or in the pyrimidin-4-ol form, with 2,7-diamido-1,8-naphthyridine (N) into a complementary heterodimer have been investigated. The formation of heterodimers with 2,7-diamido-1,8-naphthyridine from pyrimidin-4-ol dimers is much faster than from 4[1H]-pyrimidinone dimers. Using a combination of simple measurements and simulations, evidence for a bimolecular tautomerization step is presented. Finally, the acquired kinetic knowledge of the different pathways leading from ureido-pyrimidinone homodimers to ureido-pyrimidinone:diamido-naphthyridine (U:N) heterodimers allows the prediction and observation of kinetically determined ureido-pyrimidinone heterodimers which slowly convert back to the corresponding homodimers.

Oligomers based on an o-phenylene ethynylene (oPE) backbone with polar substituents have been synthesized using Sonogashira methods. Folding of these extremely short oligomers was confirmed via 1D and 2D (NOESY) NMR methods. Utilizing electron-rich and electron-poor phenylene building blocks, variations of these oPE oligomers have been synthesized to determine the folded stability of pi-rich vs pi-poor vs pi-rich-pi-poor systems. Slight variations in temperature offer a route, aside from solvent denaturation, to probe the stability of the folded structure. This is the first report of an NMR solution characterization of folding for a PE backbone without hydrogen bonds.

Three types of ribosomal preparations from Xenopus laevis eggs and embryos were tested in a cell-free system to study possible translational regulation of protein synthesis as mediated by the ribosome during early amphibian development: type 1, a crude high-speed sediment, mainly containing monoribosomes completely dissociable by 0.5 M KC1; type II, ribosomes washed with 0.5 M KC1; and type III, ribosomes treated with puromycin - 0.5 M KC1. All three types showed an active response to the addition of poly[U]. Type III was found to be the most active: levels of incorporation of 30 phenylalanine residues/ribosome were reached. In all three cases ribosomes prepared from unfertilized eggs were 30-40% less active in vitro than those from cleavage and gastrula stages.