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

Departure from randomness: Evolution of self-replicators that can self-sort through steric zipper formation

Darwinian evolution of self-replicating entities most likely played a key role in the emergence of life from inanimate matter. For evolution to occur, self-replicators must (1) have structural space accessible to them, (2) occupy only part of it at any time, and (3) navigate it through mutation and selection. We describe a system of self-replicating hexameric macrocycles formed upon the mixing of two building blocks and occupying a subset of possible sequences. Specific interactions, most likely through steric zipper formation, favor a hexamer sequence where the two blocks alternate. Under different replication-destruction regimes, distinct replicator mutants are selected. With non-selective destruction (via outflow), the fastest replicators dominate. With chemically mediated, selective destruction, a mutant that balances replication speed and resistance to reduction by steric zipper formation becomes dominant. This system demonstrates a rudimentary form of Darwinian evolution, where replicators adapt to changing selection pressures through mutation and selection.

Simultaneous Formation of a Foldamer and a Self-Replicator by Out-of-Equilibrium Dynamic Covalent Chemistry

Systems chemistry has emerged as a useful paradigm to access structures and phenomena typically exhibited by living systems, including complex molecular systems such as self-replicators and foldamers. As we progress further toward the noncovalent synthesis of life-like systems, and eventually life itself, it is necessary to gain control over assembly pathways. Dissipative chemical fueling has enabled access to stable populations of (self-assembled) structures that would normally form only transiently. Here, we report a synthetic dynamic combinatorial library, made from a single structurally simple building block, from which a self-replicator and a foldamer can emerge along two distinct and competing pathways through an inter- or intramolecular assembly process, respectively. A fueled chemical reaction cycle is then set up to generate the foldamer transiently, in the presence of the self-replicator. The partitioning of the building block between the folding and self-replication pathways and the duration of the fueled reaction cycles are controlled by adjusting the amount of the chemical fuel. An out-of-equilibrium steady state involving the two assemblies could also be achieved by using a continuous stirred tank reactor with inflow and outflow of material. This work connects the domains of folding and self-replication in synthetic systems through dissipative out-of-equilibrium chemistry. It demonstrates that foldamers and self-replicators, formed from the same building block, can stably coexist if the system is continuously supplied with energy, while at equilibrium, the Gibbs phase rule prohibits such coexistence.

Competitive exclusion among self-replicating molecules curtails the tendency of chemistry to diversify

The transition of chemistry into biology is poorly understood. Key questions include how the inherently divergent nature of chemical reactions can be curtailed, and whether Darwinian principles from biology extend to chemistry. Addressing both questions simultaneously, we now show that the evolutionary principle of competitive exclusion, which states that a single niche can be stably occupied by only one species, also applies to self-replicating chemical systems, and that this principle diminishes the tendency of chemistry to diversify. Specifically, we report two systems in which three different self-replicator quasi-species emerge in a largely stochastic fashion from a mixture of two building blocks (resources). Competitive exclusion leads to the selection of only a single quasi-species when all replicators rely to the same extent on both resources. When one of the quasi-species preferentially uses one resource and another quasi-species specializes in the other (resource partitioning), these replicator quasi-species effectively occupy different niches and were found to coexist in an evolutionary stable steady state.

Mutualistic Synthesis from Orthogonal Dynamic Covalent Reactions

Mutualisms are interactions that benefit all species involved. It has been widely investigated in neighbouring subjects, such as biology, ecology, sociology, and economics. However, such a reciprocal relationship in synthetic chemical systems has rarely been studied. Here, we demonstrate a mutualistic synthesis where byproducts from two orthogonal chemical reactions aid each other's production. Disulfide exchange and hydrazone exchange were chosen to generate two dynamic combinatorial libraries. A minor tetrameric macrocycle from the active disulfide library was quantitatively amplified in the presence of the hydrazone library. This incorporation also turned on the previously inert hydrazone reaction, producing a linear species that formed a "handcuffs" catenane with the disulfide tetramer. These findings not only lend robust support to the hypothesis of "RNA-peptide coevolution" for the origin of life but also broaden the scope of synthetic chemistry, highlighting the untapped potential of minor products from different reactions. Additionally, the co-self-assembly of these mutualistic entities to form supramolecular structures opens new avenues for future development of composite nanosystems with synergistic properties.

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.

Artificial Homeostasis Systems Based on Feedback Reaction Networks: Design Principles and Future Promises

Feedback-controlled chemical reaction networks (FCRNs) are indispensable for various biological processes, such as cellular mechanisms, patterns, and signaling pathways. Through the intricate interplay of many feedback loops (FLs), FCRNs maintain a stable internal cellular environment. Currently, creating minimalistic synthetic cells is the long-term objective of systems chemistry, which is motivated by such natural integrity. The design, kinetic optimization, and analysis of FCRNs to exhibit functions akin to those of a cell still pose significant challenges. Indeed, reaching synthetic homeostasis is essential for engineering synthetic cell components. However, maintaining homeostasis in artificial systems against various agitations is a difficult task. Several biological events can provide us with guidelines for a conceptual understanding of homeostasis, which can be further applicable in designing artificial synthetic systems. In this regard, we organize our review with artificial homeostasis systems driven by FCRNs at different length scales, including homogeneous, compartmentalized, and soft material systems. First, we stretch a quick overview of FCRNs in different molecular and supramolecular systems, which are the essential toolbox for engineering different nonlinear functions and homeostatic systems. Moreover, the existing history of synthetic homeostasis in chemical and material systems and their advanced functions with self-correcting, and regulating properties are also emphasized.

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.