Dieter Braun

Nonequilibrium selection pressures were proposed for forming oligonucleotides with rich functionalities encoded in their sequences, such as catalysis. Since phase separation was shown to direct various chemical processes, we ask whether condensed phases can provide mechanisms for sequence selection. To answer this question, we use nonequilibrium thermodynamics and describe the reversible oligomerization of different monomers to sequences at nondilute conditions prone to phase separation. We find that as sequences form, their interactions can trigger phase separation, which in turn enriches some sequences while depleting others. Our main result is that phase separation creates a selection pressure leading to specific sequence patterns when fragmentation maintains the system away from equilibrium. When fragmentation is slow, alternating sequences that interact more cooperatively with their surroundings are preferred. When fragmentation is fast, sequences with longer repeating motifs capable of more specific interactions are selected instead. Our finding that out-of-equilibrium condensed phases can provide a selection mechanism highlights their potential as versatile hubs for the evolution of functional sequences, a question relevant to the molecular origin of life and de novo life.

Phosphorus is essential for extant and nascent life. However, phosphate’s low terrestrial abundance and the poor aqueous solubility of phosphorus-bearing minerals pose major hurdles for prebiotic chemistry. Here, we show that silicate-phosphate immiscibility in volcanic melts could have provided a widely available mechanism for the local enrichment of phosphate. Starting with a phosphorus-enriched Archean melt, we observe that rapid cooling results in the formation of immiscible glassy droplets with up to 21 weight % phosphorus pentoxide, which can be delivered to the surface by volcanic processes. In aqueous leaching, we detect millimolar phosphate concentrations, which enable the synthesis of phosphorylating agents such as polyphosphates and imidazole phosphate with up to 34% yield. These results demonstrate how volcanic processes can enrich phosphate to fuel prebiotic chemistry.

Nucleic acid replication is a central process at the origin of life. On early Earth, replication is challenged by the dilution of molecular building blocks and the difficulty of separating daughter from parent strands, a necessity for exponential replication. While thermal gradient systems have been shown to address these problems, elevated temperatures lead to degradation. Also, compared to constant temperature environments, such systems are rare. The isothermal system studied here models an abundant geological environment of the prebiotic Earth, in which water is continuously evaporated at the point of contact with the gas flows, inducing up-concentration and circular flow patterns at the gas-water interface through momentum transfer. We show experimentally that this setting drives a 30-fold accumulation of nucleic acids and their periodic separation by a threefold reduction in salt and product concentration. Fluid dynamic simulations agree with observations from tracking fluorescent beads. In this isothermal system, we were able to drive exponential DNA replication with Taq polymerase. The results provide a model for a ubiquitous non-equilibrium system to host early Darwinian molecular evolution at constant temperature.

The spontaneous formation of RNA polymers is a fundamental yet challenging step for the origin of life. Here we show that 2',3'-cyclic nucleotides of all four nucleobases efficiently polymerize without external activators when subjected to wet-dry cycling at room temperature in a mild alkaline pH range. We found conditions where oligomerization yields (Y) are enhanced by wet-dry cycling, reaching Y ≈ 70% for guanosine and Y ≥ 20% for other nucleobases. Microscopy monitoring during the drying process indicates that guanosine's higher reactivity stems from its self-assembly propensity at pH ≤ 10. At pH 11, guanosine ordering is disfavored, leading to a nearly stoichiometrically balanced polymerization of the four nucleotides with Y = 36%. Only water is added at each cycle, mimicking humid nights and dry days on early Earth. This leads to a broad distribution of A, U, G, and C mixed sequence oligomers, up to 6% of 4-mer and 0.1% of 10-mer, paving the way for RNA replication and evolution through subsequent templated ligation under the same pH. The combination of simple boundary conditions and a pathway toward RNA evolution makes this process a compelling model for the prebiotic origin of RNA on early Earth.

In living cells, a complex mixture of biomolecules is assembled within and across membranes. This non-equilibrium state is maintained by sophisticated protein machinery, which imports food molecules, removes waste products and orchestrates cell division. However, it remains unclear how this complex cellular machinery emerged and evolved. Here we show how the molecular contents of a cell can be coupled in a coordinated way to non-equilibrium heat flow. A temperature difference across a water-filled pore assembled the core components of a modern cell, which could then activate the gene expression. The mechanism arose from the interplay of convection and thermophoresis, both driven by the same heat source. The cellular machinery of protein synthesis from DNA via RNA was triggered as a direct result of the concentration of cell components. The same non-equilibrium setting continued to attract food molecules from an adjacent fluid stream, keeping the cellular molecules in a confined pocket protected against diffusion. Our results show how a simple non-equilibrium physical process can assemble the many different molecules of a cell and trigger its basic functions. The framework provides a membrane-free environment to bridge the long evolutionary times from an RNA world to a protein-based cell-like proto-metabolism.

RNA and proteins are the foundation of life and a natural starting point to explore its origins. However, the prebiotic relationship between the two is asymmetric. While RNA evolved to assemble proteins from amino acids, a significant mirror-symmetric effect of amino acids to trigger the synthesis of RNA was missing. We describe ambient alkaline conditions where amino acids, without additional chemical activators, promote RNA copolymerisation more than 100-fold, starting from prebiotically plausible ribonucleoside-2′,3′-cyclic phosphates. The observed effect is explained by acid-base catalysis, with optimal efficiency at pH values near the amine pK _aH. The fold-change in oligomerisation yield is nucleobase-selective, resulting in increased compositional diversity necessary for subsequent molecular evolution and favouring the formation of natural 3′−5′ linkages. The elevated pH offers recycling of oligonucleotide sequences back to 2′,3′-cyclic phosphates, providing conditions for high-fidelity replication by templated ligation. The findings reveal a clear functional role of amino acids in the evolution of RNA earlier than previously assumed.

Phosphorus is an essential building block of life, likely since its beginning. Despite this importance for prebiotic chemistry, phosphorus was scarce in Earth’s rock record and mainly bound in poorly soluble minerals, with the calcium-phosphate mineral apatite as key example. While specific chemical boundary conditions have been considered to address this so-called phosphate problem, a fundamental process that solubilizes and enriches phosphate from geological sources remains elusive. Here, we show that ubiquitous heat flows through rock cracks can liberate phosphate from apatite by the selective removal of calcium. Phosphate’s strong thermophoresis not only achieves its 100-fold up-concentration in aqueous solution, but boosts its solubility by two orders of magnitude. We show that the heat-flow-solubilized phosphate can feed the synthesis of trimetaphosphate, increasing the conversion 260-fold compared to thermal equilibrium. Heat flows thus enhance solubility to unlock apatites as phosphate source for prebiotic chemistry, providing a key to early life’s phosphate problem.

The spontaneous formation of RNA polymers is one of the most crucial yet unsolved steps in the investigation of the origin of life. RNA oligomerization from nucleotide solutions has so far been reported only with low reactivity. Here we show that 2’,3’-cyclic nucleotides of all four nucleobases efficiently polymerize without external activators when dehydrated at room temperature in a mild alkaline pH range. Oligomerization yield, Y, and the polymer length further increase by wet-dry cycling, peaking at Y ≈ 70% in guanosine solutions and Y ≥ 20% for the other nucleobases when individually solubilized. Microscopy observation during drying indicates that the guanosine reactivity is enhanced over the other nucleobases by its self-assembly propensity. We show that at pH 11, a condition disfavoring guanosine structuring, polymerization in stoichiometrically balanced solution of the four nucleotides reaches Y = 36% and well distributed inclusion of nucleobases in the chains. The simplicity of the procedure, where only water is added at each cycle, makes this process a promising candidate for the prebiotic origin of RNA oligomers on early Earth.

RNA is an information‐carrying molecule that instructs protein synthesis, but it also functions as a catalyst in so‐called ribozymes. Here, we study this multifunctional character using a dynamic combinatorial library powered by chemical fuel. On the one hand, we demonstrate that RNA templates the oligomerization and inhibits deoligomerization. On the other hand, we show that RNA can be a structural element in the formation of hydrogels. Moreover, in its hydrogel, RNA degradation by nucleases is accelerated. Thus, templates have a role beyond blueprints, protectors, and selectors. Template‐oligomer interactions can create new (micro)environments that might affect evolutionary dynamics.

How life developed in its earliest stages is a central but notoriously difficult question in science. The earliest lifeforms likely used a reduced set of codon sequences that were progressively completed over time, driven by chemical, physical, and combinatorial constraints. However, despite its importance for prebiotic chemistry, UV radiation has not been considered a selection pressure for the evolution of early codon sequences. In this proof-of-principle study, we quantified the UV susceptibility of large pools of DNA protogenomes and tested the timing of evolutionary incorporation of codon sequences using a Monte Carlo method utilizing sequence-context-dependent damage rates previously determined by high throughput sequencing experiments. We traced the UV-radiation selection pressure on early protogenomes comprising a limited number of codon sequences to late protogenomes with access to all codons. The modeling showed that in just minutes under early sunlight, the choice of the first codons determined whether most of the protogenomes remained intact or became damaged entirely. The results correlated with earlier chemical models of the evolution of the genetic code. Our results show how UV could have played a crucial role in the evolution of the early genetic code for a DNA-based genome and provide the concept for future RNA-based studies.