Probing Structural Effects on Replication Efficiency through Comparative Analyses of Families of Potential Self-Replicators

Triple Adaptation of Constitutional Dynamic Networks of Imines in Response to Micellar Agents: Internal Uptake-Interfacial Localization-Shape Transition

Understanding the behavior of complex chemical reaction networks and how environmental conditions can modulate their organization as well as the associated outcomes may take advantage of the design of related artificial systems. Microenvironments with defined boundaries are of particular interest for their unique properties and prebiotic significance. Dynamic covalent libraries (DCvLs) and their underlying constitutional dynamic networks (CDNs) have been shown to be appropriate for studying adaptation to several processes, including compartmentalization. However, microcompartments (e.g., micelles) provide specific environments for the selective protection from interfering reactions such as hydrolysis and an enhanced chemical promiscuity due to the interface, governing different processes of network modulation. Different interactions between the micelles and the library constituents lead to dynamic sensing, resulting in different expressions of the network through pattern generation. The constituents integrated into the micelles are protected from hydrolysis and hence preferentially expressed in the network composition at the cost of constitutionally linked members. In the present work, micellar integration was observed for two processes: internal uptake based on hydrophobic forces and interfacial localization relying on attractive electrostatic interactions. The latter drives a complex triple adaptation of the network with feedback on the shape of the self-assembled entity. Our results demonstrate how microcompartments can enforce the expression of constituents of CDNs by reducing the hydrolysis of uptaken members, unravelling processes that govern the response of reactions networks. Such studies open the way toward using DCvLs and CDNs to understand the emergence of complexity within reaction networks by their interactions with microenvironments.

Design of Subreplicating Systems from an Existing Self-Replicating Diels-Alder Reaction System by Isosteric Replacement

The key feature of non-enzymatic self-replicating systems is the formation of catalytically active ternary complexes in which product templates direct precursors into spatial proximity to allow the formation of new covalent bonds. It is possible to create new replicating species by simply evaluating the ternary active complex of an existing replicating system and applying proper isosteric replacements. In this study, we have evaluated the formerly reported self-replicating Diels-Alder reaction having 61 and 33% selectivity for two diastereomeric replicators. An isosteric replacement on the spacer part connecting recognition and reactive sites of the maleimide component was applied by considering the symmetry of catalytically active ternary complexes, and it was shown that self-replication was conserved. Analysis of the new system showed 77 and 21% diastereoselectivity for the two new replicating species. Seeding experiments indicated autocatalytic activity of both replicators. In other words, both replicators compete with each other by catalyzing their own formation from the same reagent source. Another modification was applied by aiming selective blocking of the autocatalytic cycle of the competing diastereomer. The new system showed a diastereoselectivity of about 94% for the favored replicator. The kinetic data of both systems were analyzed by modeling with SimFit simulations.

A Molecular Replication Process Drives Supramolecular Polymerization

Supramolecular polymers are materials in which the connections between monomers in the polymer main chain are non-covalent bonds. This area has seen rapid expansion in the last two decades and has been exploited in several applications. However, suitable contiguous hydrogen-bond arrays can be difficult to synthesize, placing some limitations on the deployment of supramolecular polymers. We have designed a hydrogen-bonded polymer assembled from a bifunctional monomer composed of two replicating templates separated by a rigid spacer. This design allows the autocatalytic formation of the polymer main chain through the self-templating properties of the replicators and drives the synthesis of the bifunctional monomer from its constituent components in solution. The template-directed 1,3-dipolar cycloaddition reaction between nitrone and maleimide proceeds with high diastereoselectivity, affording the bifunctional monomer. The high binding affinity between the self-complementary replicating templates that allows the bifunctional monomer to polymerize in solution is derived from the positive cooperativity associated with this binding process. The assembly of the polymer in solution has been investigated by diffusion-ordered NMR spectroscopy. Both microcrystalline and thin films of the polymeric material can be prepared readily and have been characterized by powder X-ray diffraction and scanning electron microscopy. These results demonstrate that the approach described here is a valid one for the construction of supramolecular polymers and can be extended to systems where the rigid spacer between the replicating templates is replaced by one carrying additional function.

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.

Self-replicating systems

A review covering the previous 25 years study into self-replicating systems.

A recognition-mediated reaction drives amplification within a dynamic library

A single, appropriately designed, recognition event targets and transforms one of two reactive members of an exchanging pool of compounds through a recognition-mediated irreversible cycloaddition reaction, altering dramatically the final composition and kinetic behaviour of the dynamic library.

Chromosomes. CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere

Inheritance of each chromosome depends upon its centromere. A histone H3 variant, centromere protein A (CENP-A), is essential for epigenetically marking centromere location. We find that CENP-A is quantitatively retained at the centromere upon which it is initially assembled. CENP-C binds to CENP-A nucleosomes and is a prime candidate to stabilize centromeric chromatin. Using purified components, we find that CENP-C reshapes the octameric histone core of CENP-A nucleosomes, rigidifies both surface and internal nucleosome structure, and modulates terminal DNA to match the loose wrap that is found on native CENP-A nucleosomes at functional human centromeres. Thus, CENP-C affects nucleosome shape and dynamics in a manner analogous to allosteric regulation of enzymes. CENP-C depletion leads to rapid removal of CENP-A from centromeres, indicating their collaboration in maintaining centromere identity.

Supramolecular catalysis. Part 2: artificial enzyme mimics

The design of artificial catalysts able to compete with the catalytic proficiency of enzymes is an intense subject of research. Non-covalent interactions are thought to be involved in several properties of enzymatic catalysis, notably (i) the confinement of the substrates and the active site within a catalytic pocket, (ii) the creation of a hydrophobic pocket in water, (iii) self-replication properties and (iv) allosteric properties. The origins of the enhanced rates and high catalytic selectivities associated with these properties are still a matter of debate. Stabilisation of the transition state and favourable conformations of the active site and the product(s) are probably part of the answer. We present here artificial catalysts and biomacromolecule hybrid catalysts which constitute good models towards the development of truly competitive artificial enzymes.

Cellular uptake of octaarginine-conjugated tetraarylporphyrin included by per-O-methylated β-cyclodextrin

This paper describes the synthesis, structural characterization and cellular uptake of a supramolecular 1 : 2 inclusion complex of meso-tetraphenylporphyrin having an octaarginine peptide chain (R8-TPP) and heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TMe-β-CD). R8-TPP was synthesized by 2 approaches: (1) on-resin conjugation of the N-terminal of octaarginine with 5-(4-carboxyphenyl)-10,15,20-triphenylporphyrin, followed by cleavage from the resin, and (2) Michael addition reaction between 5-[4-(3-maleimidopropylamido)phenyl]-10,15,20-triphenylporphyrin and cysteine-octaarginine peptide (Cys-Arg8). The R8-TPP obtained from both the approaches formed stable inclusion complexes with TMe-β-CD by which non-substituted phenyl groups at the 10- and 20-positions were included to form trans-type 1 : 2 inclusion complexes. The complexation prevented the self-aggregation of R8-TPP, which resulted in the solubilisation of R8-TPP in aqueous media. A cellular uptake study using HeLa cells showed that R8-TPP complexed with TMe-β-CD in a serum-free medium was efficiently taken up by the cells and uniformly dispersed in the cytosol. In the serum-containing medium, the R8-TPP-TMe-β-CD complex dissociated, and the serum protein bound R8-TPP. The R8-TPP-protein complex was localized in the endosomes of the cells. The cytosol-dispersed R8-TPP showed a higher photo-induced cytotoxicity than its endosome-trapped counterpart.

Elucidating the origin of diastereoselectivity in a self-replicating system: selfishness versus altruism

We have investigated a diastereoselective self-replicating system based on a cycloaddition of a fulvene derivative and a maleimide using a two-pronged approach of combining NMR spectroscopy with computational modelling. Two diastereomers are formed with identical rates in the absence of replication. When replication is enabled, one diastereomer takes over the resources as a "selfish" autocatalyst, while exploiting the competitor as a weak "altruist", resulting in a diastereoselectivity of 16:1. We applied 1D and 2D NMR spectroscopic techniques supported by ab initio chemical shifts as well as ab initio molecular dynamics simulations to study the structure and dynamics of the underlying network. This powerful combination allowed us to decipher the energetic and structural rationale behind the observed behaviour, while static computational methods currently used in the field did not.

A simple network of synthetic replicators can perform the logical OR operation

A small network of synthetic replicators is capable of responding to instructional inputs such that the output of the network is an excess of one of the replicators whenever the input contains either or both of the replicators, mirroring the OR boolean logic operation.

Structure-reactivity relationships in a recognition mediated [3+2] dipolar cycloaddition reaction

The [3+2] dipolar cycloaddition between an azide and maleimide can be accelerated by a factor of more than 100 simply by attaching complementary recognition sites to the reactive partners. This rate acceleration derives from the formation of a reactive binary complex between the azide and the maleimide. The variation of the observed rate acceleration with simple structural changes, such as adding additional rotors, should be relatively predictable. However, the application of a simple, rotor-based increment in the systems reported here is insufficient to predict reactivity correctly. Computational studies suggest that the nature of the available reaction pathways within the binary complex formed by the reactants is important in determining the reactivity of a given complex.

Target-driven selection in a dynamic nitrone library

Nitrones undergo dynamic exchange in chloroform at room temperature through two mechanisms-hydrolysis and recombination or hydroxylamine addition/elimination; this dynamic exchange is harnessed to select a nitrone-based bis(amidopyridine) receptor for diacids from a group of four nitrones through its binding to a glutaric acid-based target.