Uncovering the selection criteria for the emergence of multi-building-block replicators from dynamic combinatorial libraries

Generalist versus Specialist Self-Replicators

Darwinian evolution, including the selection of the fittest species under given environmental conditions, is a major milestone in the development of synthetic living systems. In this regard, generalist or specialist behavior (the ability to replicate in a broader or narrower, more specific food environment) are of importance. Here we demonstrate generalist and specialist behavior in dynamic combinatorial libraries composed of a peptide-based and an oligo(ethylene glycol) based building block. Three different sets of macrocyclic replicators could be distinguished based on their supramolecular organization: two prepared from a single building block as well as one prepared from an equimolar mixture of them. Peptide-containing hexamer replicators were found to be generalists, i. e. they could replicate in a broad range of food niches, whereas the octamer peptide-based replicator and hexameric ethyleneoxide-based replicator were proven to be specialists, i. e. they only replicate in very specific food niches that correspond to their composition. However, sequence specificity cannot be demonstrated for either of the generalist replicators. The generalist versus specialist nature of these replicators was linked to their supramolecular organization. Assembly modes that accommodate structurally different building blocks lead to generalist replicators, while assembly modes that are more restrictive yield specialist replicators.

Binding of Precursors to Replicator Assemblies Can Improve Replication Fidelity and Mediate Error Correction

Copying information is vital for life's propagation. Current life forms maintain a low error rate in replication, using complex machinery to prevent and correct errors. However, primitive life had to deal with higher error rates, limiting its ability to evolve. Discovering mechanisms to reduce errors would alleviate this constraint. Here, we introduce a new mechanism that decreases error rates and corrects errors in synthetic self-replicating systems driven by self-assembly. Previous work showed that macrocycle replication occurs through the accumulation of precursor material on the sides of the fibrous replicator assemblies. Stochastic simulations now reveal that selective precursor binding to the fiber surface enhances replication fidelity and error correction. Centrifugation experiments show that replicator fibers can exhibit the necessary selectivity in precursor binding. Our results suggest that synthetic replicator systems are more evolvable than previously thought, encouraging further evolution-focused experiments.

Evolution at the Origins of Life?

The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and a protocellular phase, ultimately leading to the Last Universal Common Ancestor. Most likely, the Last Universal Common Ancestor was subject to Darwinian evolution, but the question remains to what extent Darwinian evolution applies to the prebiotic and protocellular phases. In this review, we reflect on the current status of evolutionary theory in origins of life research by bringing together philosophy of science, evolutionary biology, and empirical research in the origins field. We explore the various ways in which evolutionary theory has been extended beyond biology; we look at how these extensions apply to the prebiotic development of (proto)metabolism; and we investigate how the terminology from evolutionary theory is currently being employed in state-of-the-art origins of life research. In doing so, we identify some of the current obstacles to an evolutionary account of the origins of life, as well as open up new avenues of research.

Light-driven eco-evolutionary dynamics in a synthetic replicator system

Darwinian evolution involves the inheritance and selection of variations in reproducing entities. Selection can be based on, among others, interactions with the environment. Conversely, the replicating entities can also affect their environment generating a reciprocal feedback on evolutionary dynamics. The onset of such eco-evolutionary dynamics marks a stepping stone in the transition from chemistry to biology. Yet the bottom-up creation of a molecular system that exhibits eco-evolutionary dynamics has remained elusive. Here we describe the onset of such dynamics in a minimal system containing two synthetic self-replicators. The replicators are capable of binding and activating a co-factor, enabling them to change the oxidation state of their environment through photoredox catalysis. The replicator distribution adapts to this change and, depending on light intensity, one or the other replicator becomes dominant. This study shows how behaviour analogous to eco-evolutionary dynamics-which until now has been restricted to biology-can be created using an artificial minimal replicator system.

Mismatched covalent and noncovalent templating leads to large coiled coil-templated macrocycles

Herein we describe the use of dynamic combinatorial chemistry to self-assemble complex coiled coil motifs. We amide-coupled a series of peptides designed to form homodimeric coiled coils with 3,5-dithiobenzoic acid (B) at the N-terminus and then allowed each B-peptide to undergo disulfide exchange. In the absence of peptide, monomer B forms cyclic trimers and tetramers, and thus we expected that addition of the peptide to monomer B would shift the equilibrium towards the tetramer to maximize coiled coil formation. Unexpectedly, we found that internal templation of the B-peptide through coiled coil formation shifts the equilibrium towards larger macrocycles up to 13 B-peptide subunits, with a preference for 4, 7, and 10-membered macrocycles. These macrocyclic assemblies display greater helicity and thermal stability relative to intermolecular coiled coil homodimer controls. The preference for large macrocycles is driven by the strength of the coiled coil, as increasing the coiled coil affinity increases the fraction of larger macrocycles. This system represents a new approach towards the development of complex peptide and protein assemblies.

Tailorable and Biocompatible Supramolecular-Based Hydrogels Featuring two Dynamic Covalent Chemistries

Dynamic covalent chemistry (DCC) has proven to be a valuable tool in creating fascinating molecules, structures, and emergent properties in fully synthetic systems. Here we report a system that uses two dynamic covalent bonds in tandem, namely disulfides and hydrazones, for the formation of hydrogels containing biologically relevant ligands. The reversibility of disulfide bonds allows fiber formation upon oxidation of dithiol-peptide building block, while the reaction between NH-NH₂ functionalized C-terminus and aldehyde cross-linkers results in a gel. The same bond-forming reaction was exploited for the "decoration" of the supramolecular assemblies by cell-adhesion-promoting sequences (RGD and LDV). Fast triggered gelation, cytocompatibility and ability to "on-demand" chemically customize fibrillar scaffold offer potential for applying these systems as a bioactive platform for cell culture and tissue engineering.

Selection of diverse polymorphic structures from a small dynamic molecular network controlled by the environment

The complex interplay between systems and their environment plays an important role in processes ranging from self-assembly to evolution. Polymorphism, where, from the same ingredients different products can be formed, is likely to be an important enabler for evolutionary adaptation. Environmental pressures may induce polymorphic behaviour, where different pressures result in different structural organisation. Here we show that by combining covalent and non-covalent bond formation three distinct polymorphs can emerge from the same small dynamic molecular network: vesicular aggregates, self-replicating fibres and nanoribbons, depending on the nature of the solvent environment. Additionally, a particular set of conditions allows the transient co-existence of both vesicles and fibres.

Out-of-Equilibrium Self-Replication Allows Selection for Dynamic Kinetic Stability in a System of Competing Replicators

Among the key characteristics of living systems are their ability to self-replicate and the fact that they exist in an open system away from equilibrium. Herein, we show how the outcome of the competition between two self-replicators, differing in size and building block composition, is different depending on whether the experiments are conducted in a closed vial or in an open and out-of-equilibrium replication-destruction regime. In the closed system, the slower replicator eventually prevails over the faster competitor. In a replication-destruction regime, implemented through a flow system, the outcome of the competition is reversed and the faster replicator dominates. The interpretation of the experimental observations is supported by a mass-action-kinetics model. These results represent one of the few experimental manifestations of selection among competing self-replicators based on dynamic kinetic stability and pave the way towards Darwinian evolution of abiotic systems.

Stochastic Emergence of Two Distinct Self-Replicators from a Dynamic Combinatorial Library

Unraveling how chemistry can give rise to biology is one of the greatest challenges of contemporary science. Achieving life-like properties in chemical systems is therefore a popular topic of research. Synthetic chemical systems are usually deterministic: the outcome is determined by the experimental conditions. In contrast, many phenomena that occur in nature are not deterministic but caused by random fluctuations (stochastic). Here, we report on how, from a mixture of two synthetic molecules, two different self-replicators emerge in a stochastic fashion. Under the same experimental conditions, the two self-replicators are formed in various ratios over several repeats of the experiment. We show that this variation is caused by a stochastic nucleation process and that this stochasticity is more pronounced close to a phase boundary. While stochastic nucleation processes are common in crystal growth and chiral symmetry breaking, it is unprecedented for systems of synthetic self-replicators.

An Optical Probe for Real-Time Monitoring of Self-Replicator Emergence and Distinguishing between Replicators

Self-replicating systems play an important role in research on the synthesis and origin of life. Monitoring of these systems has mostly relied on techniques such as NMR or chromatography, which are limited in throughput and demanding when monitoring replication in real time. To circumvent these problems, we now developed a pattern-generating fluorescent molecular probe (an ID-probe) capable of discriminating replicators of different chemical composition and monitoring the process of replicator formation in real time, giving distinct signatures for starting materials, intermediates, and final products. Optical monitoring of replicators dramatically reduces the analysis time and sample quantities compared to most currently used methods and opens the door for future high-throughput experimentation in protocell environments.

An Approach to the De Novo Synthesis of Life

As the remit of chemistry expands beyond molecules to systems, new synthetic targets appear on the horizon. Among these, life represents perhaps the ultimate synthetic challenge. Building on an increasingly detailed understanding of the inner workings of living systems and advances in organic synthesis and supramolecular chemistry, the de novo synthesis of life (i.e., the construction of a new form of life based on completely synthetic components) is coming within reach. This Account presents our first steps in the journey toward this long-term goal. The synthesis of life requires the functional integration of different subsystems that harbor the different characteristics that are deemed essential to life. The most important of these are self-replication, metabolism, and compartmentalization. Integrating these features into a single system, maintaining this system out of equilibrium, and allowing it to undergo Darwinian evolution should ideally result in the emergence of life. Our journey toward de novo life started with the serendipitous discovery of a new mechanism of self-replication. We found that self-assembly in a mixture of interconverting oligomers is a general way of achieving self-replication, where the assembly process drives the synthesis of the very molecules that assemble. Mechanically induced breakage of the growing replicating assemblies resulted in their exponential growth, which is an important enabler for achieving Darwinian evolution. Through this mechanism, the self-replication of compounds containing peptides, nucleobases, and fully synthetic molecules was achieved. Several examples of evolutionary dynamics have been observed in these systems, including the spontaneous diversification of replicators allowing them to specialize on different food sets, history dependence of replicator composition, and the spontaneous emergence of parasitic behavior. Peptide-based replicator assemblies were found to organize their peptide units in space in a manner that, inadvertently, gives rise to microenvironments that are capable of catalysis of chemical reactions or binding-induced activation of cofactors. Among the reactions that can be catalyzed by the replicators are ones that produce the precursors from which these replicators grow, amounting to the first examples of the assimilation of a proto-metabolism. Operating these replicators in a chemically fueled out-of-equilibrium replication-destruction regime was found to promote an increase in their molecular complexity. Fueling counteracts the inherent tendency of replicators to evolve toward lower complexity (caused by the fact that smaller replicators tend to replicate faster). Among the remaining steps on the road to de novo life are now to assimilate compartmentalization and achieve open-ended evolution of the resulting system. Success in the synthesis of de novo life, once obtained, will have far-reaching implications for our understanding of what life is, for the search for extraterrestrial life, for how life may have originated on earth, and for every-day life by opening up new vistas in the form living technology and materials.

Diels-Alder Cycloadditions for Peptide Macrocycle Formation

Macrocyclization can confer enhanced stability, target affinity, and membrane permeability to peptide scaffolds, all of which are desirable properties for chemical probes and therapeutics. A wide array of macrocyclization chemistries have been reported over the last few decades; however, these often have limited compatibility with each other and across chemical environments, thus restricting access to specific molecular properties. In an effort to address some of these limitations, we recently described the use of Diels-Alder [4 + 2] cycloadditions for peptide macrocyclization. Among the attributes of this chemistry, we demonstrated that Diels-Alder cyclization can template diverse peptide secondary structures, proceed in organic or aqueous environments, and endow improved pharmacologic properties on cyclized peptides. Here, we present synthetic processes and characterization methods for the synthesis of Diels-Alder cyclized peptides.

Self-Sorting in Dynamic Combinatorial Libraries Leads to the Co-Existence of Foldamers and Self-Replicators

Nature segregates fundamental tasks such as information storage/transmission and catalysis between two different compound classes (e.g. polynucleotides for replication and folded polyamides for catalysis). This division of labor is likely a product of evolution, raising the question of how simpler systems in which replicators and folded macromolecules co-exist may emerge in the transition from chemistry to biology. In synthetic systems, achieving co-existence of replicators and foldamers in a single molecular network remains an unsolved problem. Previous work on dynamic molecular networks has given rise to either self-replicating fibers or well-defined foldamer structures (or completely un-sorted complex systems). We report a system in which two cross-reactive dithiol (nucleobase- and peptide-based) building blocks self-sort into a replicator fiber and foldamer that both emerge spontaneously and co-exist. The self-sorting behavior remains prevalent across different building block ratios as two phases of emergence occur: replicator growth followed by foldamer formation. This is attributed to the autocatalytic formation of the replicator fiber, followed by enrichment of the system in the remaining building block, which is subsequently incorporated into a foldamer.

Chemical Fueling Enables Molecular Complexification of Self-Replicators*

Unravelling how the complexity of living systems can (have) emerge(d) from simple chemical reactions is one of the grand challenges in contemporary science. Evolving systems of self-replicating molecules may hold the key to this question. Here we show that, when a system of replicators is subjected to a regime where replication competes with replicator destruction, simple and fast replicators can give way to more complex and slower ones. The structurally more complex replicator was found to be functionally more proficient in the catalysis of a model reaction. These results show that chemical fueling can maintain systems of replicators out of equilibrium, populating more complex replicators that are otherwise not readily accessible. Such complexification represents an important requirement for achieving open-ended evolution as it should allow improved and ultimately also new functions to emerge.

Two Sides of the Same Coin: Emergence of Foldamers and Self-Replicators from Dynamic Combinatorial Libraries

The ability of molecules and systems to make copies of themselves and the ability of molecules to fold into stable, well-defined three-dimensional conformations are of considerable importance in the formation and persistence of life. The question of how, during the emergence of life, oligomerization reactions become selective and channel these reactions toward a small number of specific products remains largely unanswered. Herein, we demonstrate a fully synthetic chemical system where structurally complex foldamers and self-replicating assemblies emerge spontaneously and with high selectivity from pools of oligomers as a result of forming noncovalent interactions. Whether foldamers or replicators form depends on remarkably small differences in building block structures and composition and experimental conditions. We also observed the dynamic transformation of a foldamer into a replicator. These results show that the structural requirements/design criteria for building blocks that lead to foldamers are similar to those that lead to replicators. What determines whether folding or replication takes place is not necessarily the type of noncovalent interaction, but only whether they occur intra- or intermolecularly. This work brings together, for the first time, the fields of replicator and foldamer chemistry.

Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems

Understanding the emergence of life from (primitive) abiotic components has arguably been one of the deepest and yet one of the most elusive scientific questions. Notwithstanding the lack of a clear definition for a living system, it is widely argued that heredity (involving self-reproduction) along with compartmentalization and metabolism are key features that contrast living systems from their non-living counterparts. A minimal living system may be viewed as "a self-sustaining chemical system capable of Darwinian evolution". It has been proposed that autocatalytic sets of chemical reactions (ACSs) could serve as a mechanism to establish chemical compositional identity, heritable self-reproduction, and evolution in a minimal chemical system. Following years of theoretical work, autocatalytic chemical systems have been constructed experimentally using a wide variety of substrates, and most studies, thus far, have focused on the demonstration of chemical self-reproduction under specific conditions. While several recent experimental studies have raised the possibility of carrying out some aspects of experimental evolution using autocatalytic reaction networks, there remain many open challenges. In this review, we start by evaluating theoretical studies of ACSs specifically with a view to establish the conditions required for such chemical systems to exhibit self-reproduction and Darwinian evolution. Then, we follow with an extensive overview of experimental ACS systems and use the theoretically established conditions to critically evaluate these empirical systems for their potential to exhibit Darwinian evolution. We identify various technical and conceptual challenges limiting experimental progress and, finally, conclude with some remarks about open questions.

Automated device for continuous stirring while sampling in liquid chromatography systems

Ultra-performance liquid chromatography is a common analysis tool, and stirring is common in many laboratory setups. Here we show a device which enables continuous stirring of samples whilst inside an ultra-performance liquid chromatography system. Utilizing standard magnetic stirring bars that fit standard vials, the device allows for the automation of experimental setups that require stirring. The device is designed such that it can replace the standard sample holder and fits in its place, while being battery operated. The use of three-dimensional (3D) printing and commercially available parts enables low-effort and low-cost device production, as well as easy modifications. Testing the device was performed by video analysis and by following the kinetics of a dynamic combinatorial library that is known to be exquisitely sensitive to agitation, as a result of involving a fiber growth-breakage mechanism. Design files and schematics are provided.

A Modular Programmable Inorganic Cluster Discovery Robot for the Discovery and Synthesis of Polyoxometalates

The exploration of complex multicomponent chemical reactions leading to new clusters, where discovery requires both molecular self-assembly and crystallization, is a major challenge. This is because the systematic approach required for an experimental search is limited when the number of parameters in a chemical space becomes too large, restricting both exploration and reproducibility. Herein, we present a synthetic strategy to systematically search a very large set of potential reactions, using an inexpensive, high-throughput platform that is modular in terms of both hardware and software and is capable of running multiple reactions with in-line analysis, for the automation of inorganic and materials chemistry. The platform has been used to explore several inorganic chemical spaces to discover new and reproduce known tungsten-based, mixed transition-metal polyoxometalate clusters, giving a digital code that allows the easy repeat synthesis of the clusters. Among the many species identified in this work, the most significant is the discovery of a novel, purely inorganic W₂₄Fe^III-superoxide cluster formed under ambient conditions. The modular wheel platform was employed to undertake two chemical space explorations, producing compounds 1-4: (C₂H₈N)₁₀Na₂[H₆Fe(O₂)W₂₄O₈₂] (1, {W₂₄Fe}), (C₂H₈N)₇₂Na₁₆[H₁₆Co₈W₂₀₀O₆₆₀(H₂O)₄₀] (2, {W₂₀₀Co₈}), (C₂H₈N)₇₂Na₁₆[H₁₆Ni₈W₂₀₀O₆₆₀(H₂O)₄₀] (3, {W₂₀₀Ni₈}), and (C₂H₈N)₁₄[H₂₆W₃₄V₄O₁₃₀] (4, {W₃₄V₄}), along with many other known species, such as simple Keggin clusters and 1D {W₁₁M²⁺} chains.

From self-replication to replicator systems en route to de novo life

The process by which chemistry can give rise to biology remains one of the biggest mysteries in contemporary science. The de novo synthesis and origin of life both require the functional integration of three key characteristics - replication, metabolism and compartmentalization - into a system that is maintained out of equilibrium and is capable of open-ended Darwinian evolution. This Review takes systems of self-replicating molecules as starting points and describes the steps necessary to integrate additional characteristics of life. We analyse how far experimental self-replicators have come in terms of Darwinian evolution. We also cover models of replicator communities that attempt to solve Eigen's paradox, whereby accurate replication needs complex machinery yet obtaining such complex self-replicators through evolution requires accurate replication. Successful models rely on a collective metabolism and a way of (transient) compartmentalization, suggesting that the invention and integration of these two characteristics is driven by evolution. Despite our growing knowledge, there remain numerous key challenges that may be addressed by a combined theoretical and experimental approach.

Emergence of light-driven protometabolism on recruitment of a photocatalytic cofactor by a self-replicator

Establishing how life can emerge from inanimate matter is among the grand challenges of contemporary science. Chemical systems that capture life's essential characteristics-replication, metabolism and compartmentalization-offer a route to understanding this momentous process. The synthesis of life, whether based on canonical biomolecules or fully synthetic molecules, requires the functional integration of these three characteristics. Here we show how a system of fully synthetic self-replicating molecules, on recruiting a cofactor, acquires the ability to transform thiols in its environment into disulfide precursors from which the molecules can replicate. The binding of replicator and cofactor enhances the activity of the latter in oxidizing thiols into disulfides through photoredox catalysis and thereby accelerates replication by increasing the availability of the disulfide precursors. This positive feedback marks the emergence of light-driven protometabolism in a system that bears no resemblance to canonical biochemistry and constitutes a major step towards the highly challenging aim of creating a new and completely synthetic form of life.

Pyrroloindole-Based Dynamic Combinatorial Chemistry

We report a new class of building blocks for Dynamic Combinatorial Chemistry (DCC) based on the pyrroloindole scaffold. The attachment of l-cysteine on the α, α′ positions of the core makes the molecule suitable for disulfide exchange in aqueous dynamic combinatorial libraries (DCLs). The synthesis of the core follows a modified version of the Knoevenagel–Hemetsberger approach. The new building block (l-PI) is fluorescent (Φ = 48%) and relatively stable towards thermal and photodegradation. The chirality of the cysteine is transferred to the electron-rich pyrroloindole core. Homo- and heterochiral DCLs of l-PI with electron-deficient l- and d-naphthalenediimide (NDI) lead to similar library distributions regardless of the enantiomer used. When no salt is present, the major component is a dimer, while dimers and tetramers are obtained at increased ionic strength.

Spontaneous Emergence of Self-Replicating Molecules Containing Nucleobases and Amino Acids

The conditions that led to the formation of the first organisms and the ways that life originates from a lifeless chemical soup are poorly understood. The recent hypothesis of “RNA-peptide coevolution” suggests that the current close relationship between amino acids and nucleobases may well have extended to the origin of life. We now show how the interplay between these compound classes can give rise to new self-replicating molecules using a dynamic combinatorial approach. We report two strategies for the fabrication of chimeric amino acid/nucleobase self-replicating macrocycles capable of exponential growth. The first one relies on mixing nucleobase- and peptide-based building blocks, where the ligation of these two gives rise to highly specific chimeric ring structures. The second one starts from peptide nucleic acid (PNA) building blocks in which nucleobases are already linked to amino acids from the start. While previously reported nucleic acid-based self-replicating systems rely on presynthesis of (short) oligonucleotide sequences, self-replication in the present systems start from units containing only a single nucleobase. Self-replication is accompanied by self-assembly, spontaneously giving rise to an ordered one-dimensional arrangement of nucleobase nanostructures.

Exploiting complexity to implement function in chemical systems

This feature article reflects a personal overview of the importance of complexity as an additional parameter to be considered in chemical research, being illustrated with selected examples in molecular recognition and catalysis.

Colloidal systems chemistry. Replication, reproduction and selection at nanoscale

Development of synthetic systems carrying life-like features is a long-standing challenge in chemistry and material science. Poor understanding of mechanisms ruling the emergence of life-like features in an inanimate matter makes the challenge even more exciting. The growing field of systems chemistry takes the lead in defining life-like dynamic signatures in minimalistic (macro)molecular systems through the development of multicomponent synthetic models using tools from organic and supramolecular chemistry. Recent progress in nanoscience makes available a range of novel materials that can undoubtedly enrich systems chemistry. Therefore, with the aim of placing nano- and colloidal science within the context of systems chemistry, the recent experimental and theoretical developments dealing with the use of nanoparticles and their assemblies in the realisation of the concepts such as replication, reproduction and selection are discussed.

Template-promoted self-replication in dynamic combinatorial libraries made from a simple building block

We report dynamic combinatorial libraries made from a simple building block that is on the verge of enabling self-assembly driven self-replication. Adding a template provides a sufficient additional push yielding self-replication. Self-assembly and self-replication can emerge with building blocks that are considerably smaller than those reported thus far.

Achieving biopolymer synergy in systems chemistry

Synthetic and materials chemistry initiatives have enabled the translation of the macromolecular functions of biology into synthetic frameworks. These explorations into alternative chemistries of life attempt to capture the versatile functionality and adaptability of biopolymers in new orthogonal scaffolds. Information storage and transfer, however, so beautifully represented in the central dogma of biology, require multiple components functioning synergistically. Over a single decade, the emerging field of systems chemistry has begun to catalyze the construction of mutualistic biopolymer networks, and this review begins with the foundational small-molecule-based dynamic chemical networks and peptide amyloid-based dynamic physical networks on which this effort builds. The approach both contextualizes the versatile approaches that have been developed to enrich chemical information in synthetic networks and highlights the properties of amyloids as potential alternative genetic elements. The successful integration of both chemical and physical networks through β-sheet assisted replication processes further informs the synergistic potential of these networks. Inspired by the cooperative synergies of nucleic acids and proteins in biology, synthetic nucleic-acid-peptide chimeras are now being explored to extend their informational content. With our growing range of synthetic capabilities, structural analyses, and simulation technologies, this foundation is radically extending the structural space that might cross the Darwinian threshold for the origins of life as well as creating an array of alternative systems capable of achieving the progressive growth of novel informational materials.

Existing Self-Replicators Can Direct the Emergence of New Ones

The study of the interplay between different self-replicating molecules constitutes an important new phase in the synthesis of life and in unravelling the origin of life. Here we show how existing replicators can direct the nature of a newly formed replicator. Starting from the same building block, 6-ring replicators formed when the mixture was exposed to pre-existing 6-membered replicators, while pre-formed 8-membered replicators funneled the building block into 8-ring replicators. Not only ring size, but also the mode of assembly of the rings into stacks was inherited from the pre-existing replicators. These results show that the nature of self-replicating molecules can be strongly influenced by the interplay between different self-replicators, overriding preferences innate to the structure of the building block.

Parasitic Behavior of Self-Replicating Molecules

Self-replication plays a central role in the origin of life and in strategies to synthesize life de novo. Studies on self-replication have focused mostly on isolated systems, while the dynamics of systems containing multiple replicators have received comparatively little attention. Yet most evolutionary scenarios involve the interplay between different replicators. Here we report the emergence of parasitic behavior in a system containing self-replicators derived from two subtly different building blocks 1 and 2. Replicators from 2 form readily through cross-catalysis by pre-existing replicators made from 1. Once formed, the new replicators consume the original replicators to which they owe their existence. These results resemble parasitic and predatory behavior that is normally associated with living systems and show how such lifelike behavior has its roots in relatively simple systems of self-replicating molecules.

Fine-tuning the physicochemical properties of peptide-based blood-brain barrier shuttles

N-methylation is a powerful method to modify the physicochemical properties of peptides. We previously found that a fully N-methylated tetrapeptide, Ac-(N-MePhe)₄-CONH₂, was more lipophilic than its non-methylated analog Ac-(Phe)₄-CONH₂. In addition, the former crossed artificial and cell membranes while the latter did not. Here we sought to optimize the physicochemical properties of peptides and address how the number and position of N-methylated amino acids affect these properties. To this end, 15 analogs of Ac-(Phe)₄-CONH₂ were designed and synthesized in solid-phase. The solubility of the peptides in water and their lipophilicity, as measured by ultra performance liquid chromatography (UPLC) retention times, were determined. To study the permeability of the peptides, the Parallel Artificial Membrane Permeability Assay (PAMPA) was used as an in vitro model of the blood-brain barrier (BBB). Contrary to the parent peptide, the 15 analogs crossed the artificial membrane, thereby showing that N-methylation improved permeability. We also found that N-methylation enhanced lipophilicity but decreased the water solubility of peptides. Our results showed that both the number and position of N-methylated residues are important factors governing the physicochemical properties of peptides. There was no correlation between the number of N-methylated amide bonds and any of the properties measured. However, for the peptides consecutively N-methylated from the N-terminus to the C-terminus (p1, p5, p11, p12 and p16), lipophilicity correlated well with the number of N-methylated amide bonds and the permeability of the peptides. Moreover, the peptides were non-toxic to HEK293T cells, as determined by the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay.

Exploring the emergence of complexity using synthetic replicators

A significant number of synthetic systems capable of replicating themselves or entities that are complementary to themselves have appeared in the last 30 years. Building on an understanding of the operation of synthetic replicators in isolation, this field has progressed to examples where catalytic relationships between replicators within the same network and the extant reaction conditions play a role in driving phenomena at the level of the whole system. Systems chemistry has played a pivotal role in the attempts to understand the origin of biological complexity by exploiting the power of synthetic chemistry, in conjunction with the molecular recognition toolkit pioneered by the field of supramolecular chemistry, thereby permitting the bottom-up engineering of increasingly complex reaction networks from simple building blocks. This review describes the advances facilitated by the systems chemistry approach in relating the expression of complex and emergent behaviour in networks of replicators with the connectivity and catalytic relationships inherent within them. These systems, examined within well-stirred batch reactors, represent conceptual and practical frameworks that can then be translated to conditions that permit replicating systems to overcome the fundamental limits imposed on selection processes in networks operating under closed conditions. This shift away from traditional spatially homogeneous reactors towards dynamic and non-equilibrium conditions, such as those provided by reaction-diffusion reaction formats, constitutes a key change that mimics environments within cellular systems, which possess obvious compartmentalisation and inhomogeneity.

Emergence of a New Self-Replicator from a Dynamic Combinatorial Library Requires a Specific Pre-Existing Replicator

Our knowledge regarding the early steps in the formation of evolvable life and what constitutes the minimal molecular basis of life remains far from complete. The recent emergence of systems chemistry reinvigorated the investigation of systems of self-replicating molecules to address these questions. Most of these studies focus on single replicators and the effects of replicators on the emergence of other replicators remains under-investigated. Here we show the cross-catalyzed emergence of a novel self-replicator from a dynamic combinatorial library made from a threonine containing peptide building block, which, by itself, only forms trimers and tetramers that do not replicate. Upon seeding of this library with different replicators of different macrocycle size (hexamers and octamers), we observed the emergence of hexamer replicator consisting of six units of the threonine peptide only when it is seeded with an octamer replicator containing eight units of a serine building block. These results reveal for the first time how a new replicator can emerge in a process that relies critically on the assistance by another replicator through cross-catalysis and that replicator composition is history dependent.

Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles

Self-replication at the molecular level is often seen as essential to the early origins of life. Recently a mechanism of self-replication has been discovered in which replicator self-assembly drives the process. We have studied one of the examples of such self-assembling self-replicating molecules to a high level of structural detail using a combination of computational and spectroscopic techniques. Molecular Dynamics simulations of self-assembled stacks of peptide-derived replicators provide insights into the structural characteristics of the system and serve as the basis for semiempirical calculations of the UV-vis, circular dichroism (CD) and infrared (IR) absorption spectra that reflect the chiral organization and peptide secondary structure of the stacks. Two proposed structural models are tested by comparing calculated spectra to experimental data from electron microscopy, CD and IR spectroscopy, resulting in a better insight into the specific supramolecular interactions that lead to self-replication. Specifically, we find a cooperative self-assembly process in which β-sheet formation leads to well-organized structures, while also the aromatic core of the macrocycles plays an important role in the stability of the resulting fibers.

Grip on complexity in chemical reaction networks

A new discipline of "systems chemistry" is emerging, which aims to capture the complexity observed in natural systems within a synthetic chemical framework. Living systems rely on complex networks of chemical reactions to control the concentration of molecules in space and time. Despite the enormous complexity in biological networks, it is possible to identify network motifs that lead to functional outputs such as bistability or oscillations. To truly understand how living systems function, we need a complete understanding of how chemical reaction networks (CRNs) create function. We propose the development of a bottom-up approach to design and construct CRNs where we can follow the influence of single chemical entities on the properties of the network as a whole. Ultimately, this approach should allow us to not only understand such complex networks but also to guide and control their behavior.

Serotyping, antibiotic susceptibility, and virulence genes screening of Escherichia coli isolates obtained from diarrheic buffalo calves in Egyptian farms

AIM

In Egypt as in many other countries, river water buffalo (Bubalus bubalis) is considered an important source of high-quality milk and meat supply. The objective of this study was to investigate serotypes, virulence genes, and antibiotic resistance determinants profiles of Escherichia coli isolated from buffalo at some places in Egypt; noticibly, this issue was not discussed in the country yet.

MATERIALS AND METHODS

A number of 58 rectal samples were collected from diarrheic buffalo calves in different regions in Egypt, and bacteriological investigated for E. coli existence. The E. coli isolates were biochemically, serologicaly identified, tested for antibiotic susceptibility, and polymerase chain reaction (PCR) analyzed for the presence of antibiotic resistance determinants and virulence genes.

RESULTS

Overall 14 isolates typed as E. coli (24.1%); 6 were belonged to serogroup O78 (10.3%), followed by O125 (4 isolates, 6.9%), then O158 (3 isolates, 5.2%) and one isolate O8 (1.7%), among them, there were 5 E. coli isolates showed a picture of hemolysis (35.7%). The isolates exhibited a high resistance to β lactams over 60%, followed by sulfa (50%) and aminoglucoside (42.8%) group, in the same time the isolates were sensitive to quinolone, trimethoprim-sulfamethoxazole, tetracycline (100%), and cephalosporine groups (71.4%). A multiplex PCR was applied to the 14 E. coli isolates revealed that all were carrying at least one gene, as 10 carried blaTEM (71.4%), 8 Sul1 (57.1%), and 6 aadB (42.8%), and 9 isolates could be considered multidrug resistant (MDR) by an incidence of 64.3%. A PCR survey was stratified for the most important E. coli virulence genes, and showed the presence of Shiga toxins in 9 isolates carried either one or the two Stx genes (64.3%), 5 isolates carried hylA gene (35.7%), and eae in 2 isolates only (14.3%), all isolates carried at least one virulence gene except two (85.7%).

CONCLUSION

The obtained data displayed that in Egypt, buffalo as well as other ruminants could be a potential source of MDR pathogenic E. coli variants which have a public health importance.

Towards open-ended evolution in self-replicating molecular systems

In this review we discuss systems of self-replicating molecules in the context of the origin of life and the synthesis of de novo life. One of the important aspects of life is the ability to reproduce and evolve continuously. In this review we consider some of the prerequisites for obtaining unbounded evolution of self-replicating molecules and describe some recent advances in this field. While evolution experiments involving self-replicating molecules have shown promising results, true open-ended evolution has not been realized so far. A full understanding of the requirements for open-ended evolution would provide a better understanding of how life could have emerged from molecular building blocks and what is needed to create a minimal form of life in the laboratory.

Self-Assembly Can Direct Dynamic Covalent Bond Formation toward Diversity or Specificity

With the advent of reversible covalent chemistry the study of the interplay between covalent bond formation and noncovalent interactions has become increasingly relevant. Here we report that the interplay between reversible disulfide chemistry and self-assembly can give rise either to molecular diversity, i.e., the emergence of a unprecedentedly large range of macrocycles or to molecular specificity, i.e., the autocatalytic emergence of a single species. The two phenomena are the result of two different modes of self-assembly, demonstrating that control over self-assembly pathways can enable control over covalent bond formation.

Multiple competing pathways for chemical reaction: drastic reaction shortcut for the self-catalytic double-helix formation of helicene oligomers

Competition among multiple pathways in a chemical reaction exhibits notable kinetic phenomena, particularly when amplification by self-catalysis is involved. A pseudoenantiomeric 1 : 1 mixture of an aminomethylene helicene (P)-tetramer and an (M)-pentamer formed enantiomeric hetero-double helices B and C in solution when random coil A was cooled. When a solution of A at 70 °C was directly cooled to 25 °C, the A-to-B reaction was predominant, then B was slowly converted to C over 60 h. The slow conversion in the A-to-B-to-C reaction was due to the formation of the hetero-double helix B, which was an off-pathway intermediate, and the slow B-to-C conversion. In contrast, when a solution of A at 70 °C was snap-cooled to -25 °C before then maintaining the solution at 25 °C, the A-to-C reaction predominated, and the formation of C was complete within 4 h. The reactions involve competition between the self-catalytic A-to-B and A-to-C pathways, where B and C catalyze the A-to-B and A-to-C reactions, respectively. Subtle differences in the initial states generated by thermal pretreatment were amplified by the self-catalytic process, which resulted in a drastic reaction shortcut.

Systems chemistry

A series of exciting phenomena that can occur in supramolecular systems away from equilibrium are reviewed.