From Polymerization-Enabled Folding and Assembly to Chemical Evolution: Key Processes for Emergence of Functional Polymers in the Origin of Life

1. Introduction

Understanding how life arose spontaneously from nonliving matter on Earth, and how it might emerge elsewhere in the Universe, remains a grand scientific challenge. A central goal in the field of prebiotic chemistry is to understand mechanisms for the spontaneous emergence of self-sustaining and informational chemical systems. Based on analogies to biology, it seems likely that such systems would have required covalent polymers with building blocks of specific classes (e.g., amino acids, nucleotides, sugars) as well as the selective association of these molecules through noncovalent interactions to generate supramolecular assemblies. This review is intended to provide an overview of fundamental abiotic processes that can act on the building blocks of life, or their predecessor molecules, to bring about increasing organization and functionality as a probable outcome. We focus on the coupling of building blocks to form polymers, folding and association of polymers to form molecular assemblies, and selection within evolving chemical systems to drive the emergence of various functionalities that would become sustained by their associated chemical networks.

2. The Tapestry of Biochemistry Is Woven with Polymers

Life on Earth requires polymers—proteins, nucleic acids, polysaccharides, and lipids. These large molecules are constructed by covalently linking monomeric building blocks (amino acids, nucleotides, sugars, and fatty acids) into larger chains (Fig. 1). Whereas proteins and nucleic acids are assembled as linear chains, polysaccharides can be linear or branched, and lipids generally contain two or three fatty acids linked by a glycerol unit. Life’s polymers provide mechanical structure and compartmentalization, catalyze reactions, organize metabolic processes, and store/transduce information and energy, among other functions. Given the central role of polymers in known biochemistry and their apparent optimization of structures for specific functions, it seems certain that primordial polymers played a foundational role in the origins of life. The earliest polymers were not necessarily the same as those that biology uses today and were probably more heterogeneous in nature due to the presumed “messiness” and diverse chemical space of the prebiotic environment.

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FIG. 1.

Biopolymer synthesis and structure. Proteins, polysaccharides, nucleic acids, and lipids are formed via condensation reactions that release water to join together their respective building blocks. Breakdown of the biopolymers, for monomer recycling, proceeds via hydrolysis reactions—the reverse of the polymerization reaction. Remarkably, seven distinct types of condensation–dehydration reactions are involved in the routes of biopolymer synthesis shown. The reactions shown are intended merely to illustrate general commonalities in the synthesis of biopolymers. Prebiotic routes to biopolymers would not necessarily involve the exact processes, order of steps, or reactants shown in the figure.

Biopolymers have remarkable emergent properties (Runnels et al., 2018):

Polymers composed of even a small number of distinct monomeric units of a specific class provide efficient access to an enormous compositional and functional diversity. In the case of extant biology, the four d-nucleotides of DNA are able to store the information required to encode every living organism on Earth, and the 20 proteinogenic l-amino acids can code for more proteins than could ever be made, given all the organic matter in the known Universe.

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FIG. 2.

Polymerization promotes the formation of folded molecular assemblies in macromolecules. (a) Covalent coupling of monomers into polymers constrains the individual building blocks to be in close proximity with fewer degrees of freedom. Although a single associated structure is shown for simplicity, in reality, multiple noncovalent assemblies or folded conformations will be sampled. (b) Schematic representation of various folded motifs in biopolymer classes. Biopolymers can fold into a variety of secondary, tertiary, and quaternary structures, depending on the sequence of the polymer.

A relatively complete set of building blocks that comprise today’s biopolymers—sugars, amino acids, nucleobases, and fatty acids—are believed to have existed on prebiotic Earth (Johnson et al., 2008; Meierhenrich et al., 2004; Patel et al., 2015; Ruiz-Bermejo et al., 2007; Zaia et al., 2008). A wide variety of amino acids were likely present, both via production in situ (Lawless and Boynton, 1973; Miller, 1953, 1974; Miller et al., 1976; Parker et al., 2011; Ring et al., 1972) and via exogenous delivery (Elsila et al., 2016; Miller et al., 1976; Wolman et al., 1972). While the proteinogenic amino acids are all α-amino acids of enantiomerically pure l-configuration, the prebiotic milieu would have contained a more diverse set of racemic amino acids, functional groups, and isomeric forms (e.g., α-, β-, and γ-amino acids) (Elsila et al., 2016; Frenkel-Pinter et al., 2020b; Miller, 1987; Miller et al., 1976; Polanco et al., 2013; Zaia et al., 2008). Sugars are found in some meteorites (Furukawa et al., 2019) and can be produced in model prebiotic reactions such as the formose reaction, which produces C3–C6 carbohydrates (Butlerow, 1861; Cleaves II, 2008; Meinert et al., 2016; Robinson et al., 2022). Fatty acids are found in model prebiotic reactions via Fischer–Tropsch-type synthesis (Morigaki and Walde, 2007; Proskurowski et al., 2008) and have been found in meteorites (Lawless and Yuen, 1979; Schmitt-Kopplin et al., 2010). While it was recently suggested that phospholipids akin to those found in cellular membranes formed abiotically (Bonfio et al., 2019; Gibard et al., 2018, 2019), it is still widely considered more likely that the first membranes were composed of simpler amphiphiles, such as fatty acids (Deamer et al., 2002; Morigaki and Walde, 2007).

5. How Did the First Polymers Form?

Proteins, nucleic acids, and polysaccharides are all biosynthesized via condensation–dehydration reactions (Fig. 1), which release a water molecule as a side product when a covalent bond is formed between two monomeric building blocks or their oligomers. These reactions are thermodynamically unfavorable in water at ambient temperature and pressure, and given sufficient time all biopolymers will spontaneously hydrolyze in water (Runnels et al., 2018). These facts have been perceived as a problem for prebiotic chemical scenarios, because the polymers necessary for life are energetically costly to produce and are chemically unstable in water. In biology, condensation reactions are catalyzed by enzymes and energetically driven by coupling condensation reactions to the scission of high-energy pyrophosphate bonds. Of course, enzymes and sophisticated metabolic coupling were not available on the prebiotic Earth. These observations, similar to many others associated with the spontaneous emergence of life, present a conundrum: How could the earliest polymers have been generated without evolved enzymes and against the unfavorable thermodynamics of high water activity (Ross and Deamer, 2019)?

6. General Mechanisms of Prebiotic Polymerization

A number of proposals to overcome the difficulty of prebiotic polymer synthesis have been put forward (Frenkel-Pinter et al., 2020b; Kitadai and Maruyama, 2018; Ruiz-Mirazo et al., 2014; Sutherland, 2017; Whitaker and Powner, 2024). The most explored routes can be divided into two main categories: thermal processes (including wet–dry cycling) and chemical activation of building blocks with the use of chemical condensing agents. These driving forces are not mutually exclusive and certainly could have complemented each other on early Earth. Environments with alternative solvents or low water activity may have also facilitated prebiotic polymer formation (Campbell et al., 2019; He et al., 2017; Lozoya-Colinas et al., 2022; Rode, 1999). Short polymers (oligomers) can covalently join together to generate longer functional molecules in a process known as fragment ligation (Canavelli et al., 2019; Lee et al., 1996; Liu et al., 2019). Ultimately, there likely was a dynamic flux of oligomer concentrations dependent on the environment, resulting from continuous oligomer generation due to dehydration reactions and oligomer breakdown due to spontaneous hydrolysis.

i.

Thermal mechanisms of oligomer formation. Heating and drying monomeric building blocks is conceptually the simplest way to drive polymerization by condensation reactions, an approach that has been explored since the earliest attempts to polymerize amino acids (Fox and Harada, 1958). The processes of heating, drying, and wet–dry cycling to drive monomer oligomerization have now been reported for each of the main biopolymer classes, but these reactions generally produce low yields and relatively short oligomer lengths (Forsythe et al., 2015; Fox and Harada, 1958; Li et al., 2019; Matreux et al., 2024; Rodriguez-Garcia et al., 2015; Verlander et al., 1973). These reactions are also often complicated by the formation of side products, lack of regioselectivity, and varying degrees of degradation of the reactants and/or products. Moreover, periods in a hot, dry state could have hindered nascent life by allowing exposure to damaging radiation, degradation of organic molecules, and disruption of membranes.

ii.

Condensing agents. Certain high-energy chemical reagents called condensing agents can be used to drive otherwise unfavorable oligomerization reactions. Several potentially prebiotic condensing agents have been reported (Frenkel-Pinter et al., 2020b; Kitadai and Maruyama, 2018; Ruiz-Mirazo et al., 2014). Given that proteins, nucleic acids, and polysaccharides are all biosynthesized using phosphorylated or pyrophosphorylated intermediates, abiotic condensing agents that act through a mechanism involving phosphorylation, such as trimetaphosphate (Chung et al., 1971) and diamidophosphate (Gibard et al., 2018), have attracted considerable interest. In general terms, potentially prebiotic condensing agents suffer similar drawbacks as the thermal processes mentioned above—typically low yields, relatively short oligomer lengths, formation of side products, and lack of regioselectivity. Moreover, the possible sources and feasible concentrations of the various condensing agents on early Earth are unknown.

7. Preorganization of Monomers Can Promote the General Mechanisms for Oligomerization Reactions

Surfaces, interfaces, supramolecular assemblies, and molecular templates have been shown to facilitate potentially prebiotic oligomerization reactions by locally concentrating and preorganizing building blocks. Of notable relevance, the ribosome catalyzes peptide bond synthesis almost entirely through an entropic means, by appropriately organizing substrates (i.e., tRNAs) at the active site and excluding water (Sievers et al., 2004), as opposed to the greater repertoire of catalytic mechanisms used by many enzymes. The most studied mineral surfaces for promoting oligomerization are montmorillonite clays (Ferris et al., 1996; Ferris and Ertem, 1993; Lambert, 2008), although a diversity of minerals can be effective (Riggi et al., 2023). Abiotic oligomerizations can be also promoted by a much wider variety of physiochemical phenomena that concentrate and organize the reactants (An et al., 2021; Blocher et al., 1999; Deal et al., 2021; Griffith and Vaida, 2012; Kanavarioti et al., 2001; Olasagasti and Rajamani, 2019), such as collection on the surface of lipid vesicles and aerosols, sequestration between lipid bilayers in a dried multilamellar vesicle, within coacervates, at the air–water interface, and exclusion into the eutectic phases of water during ice formation. Template-directed synthesis is a process in which polymerization is promoted by preorganizing reactants along a molecular template, such as a complementary nucleic acid strand. This process has been extensively studied in the context of nucleic acid chemistry (Bohler et al., 1995; Kozlov and Orgel, 2000; Todisco et al., 2018) and to a lesser extent for certain peptides, such as the ones that can form amyloid-like or coiled-coil templates (Lee et al., 1996; Rout et al., 2018; Rubinov et al., 2009). Templated reactions can show good fidelity for the incoming complementary building block and can be fairly selective for chirality and regiochemistry.

8. Oligomers Self-Assemble via Noncovalent Interactions

The macromolecules produced by covalent polymerization processes described above can themselves fold or assemble in aqueous solution due to noncovalent intra- or intermolecular interactions. Such assemblies are crucial for many structures found in extant biology, from cell membranes and intracellular organelles to DNA duplexes and chromosomes. Water molecules are important participants in many self-assembly processes; they often provide a substantial entropic driving force as part of the hydrophobic effect (Chandler, 2005; Tanford, 1978, 1979), where the clustering of nonpolar moieties allows for the net release of water molecules from restricted orientational states at nonpolar interfaces (Nelson et al., 2017). This increase in the overall entropy of the system favors the association of nonpolar moieties in aqueous solution. Key examples include the folding of polypeptides and globular proteins around a core of tightly packed hydrophobic amino acid side chains, the stacking of nucleic acid base pairs during duplex formation, and the association of lipids into membrane bilayers.

During molecular folding and assembly, combined nonspecific and specific interactions contribute to the overall structure. Examples in extant biology include intramolecular protein compaction into specific three-dimensional folds that depend on the polypeptide sequence, as well as the intermolecular processes of DNA double helix formation via sequence complementarity (Runnels et al., 2018). The like-charged DNA backbones aid solubility and prevent irreversible association between strands, while similar but nonidentical nucleobase side chains provide binding and molecular recognition via pi-stacking and H-bonding interactions (Benner, 2004). Prebiotic informational polymers may have similarly incorporated combinations of nonspecific and specific self-assembly motifs to enable templated replication. Moreover, noncovalent supramolecular polymers may have even predated the emergence of modern nucleic acids (Karunakaran et al., 2018). Such associations can increase reaction rates by locally organizing monomers in close proximity while also protecting these assembled molecules from reactions with other molecules in solution (Edri et al., 2023; Mangalath et al., 2021; Rout et al., 2022).

9. Molecular Self-Assembly Can Generate Diverse Microcompartments

Self-assembly can also lead to larger structures such as the micron-scale lipid vesicles and biomolecular condensate droplets that organize cell interiors today (Fig. 3A, B) (Alberts et al., 2002; Hirose et al., 2023). Primitive versions of these compartments could have facilitated the emergence of life, for example, by sequestering, protecting, and concentrating molecular components to enhance catalysis, prevent parasite takeover in replication, and define individuals upon which natural selection could act (Fig. 4) (Mizuuchi and Ichihashi, 2021). Even relatively simple and heterogeneous molecules can assemble (Agazani et al., 2021; Misra et al., 2021; Reches and Gazit, 2003; Rufo et al., 2014; Singh et al., 2017; Zozulia et al., 2018). Amphiphile vesicles and coacervate droplets, described in more detail below, are two widely studied prebiotic compartments that form by assembly of broad classes of molecular components. This versatility is important given the likely heterogeneity of prebiotic molecular mixtures, which could further support changes in compartment composition and function over time in response to component availability and/or environmental conditions (Monnard and Walde, 2015).

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FIG. 3.

Prebiotically relevant microcompartments generated via molecular self-assembly. (a) Amphiphiles can self-assemble to form vesicles with an aqueous lumen. (b) Oligomers/polymers that have multiple dynamic intermolecular associations can undergo liquid–liquid phase separation to generate coacervate droplets. (c) Lipid molecules can self-assemble around a coacervate surface to form hybrid protocells that contain a coacervate lumen surrounded by a membrane boundary. Although the membrane has been shown as a defect-free bilayer in this figure for simplicity, other membrane morphologies (incomplete or multilamellar membranes) are also likely.

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FIG. 4.

Functions of prebiotic compartments. (a) Prebiotic compartments would have facilitated the emergence of cellular life by performing various functions such as sequestration, exchange, and protection of encapsulated molecules, acting as a reaction crucible, and (b) defining an individual chemical system upon which different evolutionary forces could act. One such example is shown here, where polymer-encapsulating compartments have a selective advantage over empty compartments.

Geochemical features of prebiotic niches, such as ponds and tidal pools, could have also facilitated assembly and compartmentalization (Gozen et al., 2022). For example, the conditions within a small body of water can change tremendously during cycles of evaporation and rehydration, with changes in temperature, pH, solution ionic strength, and concentrations of specific divalent metal ions (e.g., Fe²⁺ and Mg²⁺). Such changes in solution conditions can influence the formation and properties of vesicles or coacervates. For example, SCAs form vesicles above their melting temperature, which depends on their chain length, unsaturation, and the type of head group (Morigaki and Walde, 2007). Phase separation can be favored at higher or lower solution temperatures depending on the system, and transition temperatures are tunable by chemical structure (e.g., peptide sequence) (Quiroz and Chilkoti, 2015). When weak acids or weak bases are involved in assembly, the solution pH relative to the acid dissociation constant for these groups is important. Fatty acids generally require pH near their apparent pK_a to form vesicles (Morigaki and Walde, 2007), whereas micelles and disordered oil droplets are formed at higher and lower pH, respectively. Around their apparent pK_a, hydrogen bonding between the protonated and deprotonated fatty acid molecules generates pseudo-diacyl structures with a cylindrical shape that favors vesicle formation (Sarkar et al., 2020b). The ionic strength of the medium also significantly affects the ability of some SCAs to form vesicles, with high salt concentrations potentially causing SCA aggregation (Monnard et al., 2002) and complex coacervate dissolution (Cakmak et al., 2020). Wet–dry cycling can drive repeated cycles of compartmentalization and partial or complete release of contents, for example, RNA release from polyelectrolyte coacervates (Fares et al., 2020). SCAs such as fatty acids and N-acyl amino acids are particularly sensitive to divalent cations such as Mg²⁺ (Joshi et al., 2021b; Monnard et al., 2002), which is important for RNA folding and catalysis (Szostak, 2012). Metal ion chelation by ligands such as multivalent carboxylate or phosphate moieties can protect against vesicle disruption by Mg²⁺ (Adamala and Szostak, 2013). When such ligands are concentrated within coacervate droplets, high local Mg²⁺ concentrations can result (Frankel et al., 2016; Poudyal et al., 2019b).

11. From Vesicles and Coacervates to Hybrid Protocell Compartments

Compartmentalization provides a protective microenvironment to support certain reactions and creates a distinct ensemble of molecules on which a selection pressure can act (Fig. 4) (Monnard and Walde, 2015). In comparison with vesicles, coacervates are generally superior for accumulating molecules such as RNAs, concentrating them by several orders of magnitude from an otherwise dilute solution by equilibrium partitioning, which can aid ribozyme activity (Poudyal et al., 2018). However, unlike vesicles, coacervates coalesce upon contact and lack a membrane-like barrier to control access into/out of the compartment, which reduces their ability to function as individuals under selective pressure. In this context, the “messiness” of the prebiotic chemical milieu, which would have contained more complex molecular mixtures than typical laboratory experiments, may offer a solution: coacervate droplets can template the self-assembly of amphiphile membranes to generate hybrid protocells that are able to leverage the advantageous features of vesicles and coacervates while overcoming their limitations (Fig. 3C) (Cakmak et al., 2021; Dora Tang et al., 2014; Gao and Mann, 2023). Such hybrid protocells may represent an advanced stage in the evolution of primitive compartments.

12. The Possibility of Precellular Life

It is possible that nucleic acids and coded protein synthesis emerged on Earth before the involvement of vesicles with low molecular permeability, that is, before the appearance of protocells. Carl Woese, a pioneer in ribosome-based studies of early biological evolution, championed this scenario based on evidence that the earliest forms of life practiced rampant horizontal gene transfer (Woese, 2002), a process that would have been hindered by compartmentalization. Woese proposed that precellular life consisted of nucleic acids in “supramolecular aggregates.” This proposal has similarities to the abovementioned coacervates that attract RNA and the recent proposal that viscous prebiotic solvents could have facilitated nucleic acid replication and evolution by slowing template duplex reannealing during template-directed synthesis (He et al., 2017). Both systems, the former being thermodynamic in nature and the latter being kinetic in nature, provide for some degree of nucleic acid spatial/temporal segregation while not being so restrictive as to block the mixing of genetic materials. Another potential sign that persistent compartmentalization came after the emergence of nucleic acid replication and protein synthesis is the fact that the membranes of the three branches of life (bacteria, archaea, and eukaryotes) have fundamental differences in the structures of the lipids that comprise their membranes, whereas the structures of DNA, RNA, and the peptide backbone are universal features of biochemistry.

13. Difficulties Associated with Chemical Diversity

If we assume that prebiotic Earth had a rich inventory of organic building blocks, the so-called prebiotic soup, then the processes outlined above would have yielded a broad array of oligomers and noncovalent molecular assemblies. But how did this vast chemical system eventually evolve into life, rather than devolve into useless tar? How could nonbiological evolutionary processes select certain molecules with elaborate structures, properties, and functions? This is a critical and unresolved issue. Abiotic processes for the formation of organic matter often produce messy, nonspecific mixtures of compounds, which have been referred to as intractable “tar” or “asphalt” (Benner et al., 2012; Nitschke et al., 2024; Schwartz, 2007; Shapiro, 2000), whereas biology is marked by chemical homogeneity, as illustrated by its homochiral, regiospecific biopolymers. How could the uniformity found in biology arise, seemingly against the second law of thermodynamics, from processes prone toward molecular combinatorial explosion?

14. Chemical Evolution

One potential answer to the difficulties associated with chemical diversity lies in the related processes of chemical evolution and chemical selection. In the context of this review, our working definition of chemical evolution is continuous change in chemical species with exploration of new chemical space and avoidance of an equilibrium condition. Some advances in understanding chemical evolution have come from systems chemistry (Ashkenasy et al., 2017; Cafferty et al., 2019; Islam and Powner, 2017; Kroiss et al., 2019; Patel et al., 2015; Ruiz-Mirazo et al., 2014), dynamic combinatorial chemistry (DCC) (Cao et al., 2021; Komáromy et al., 2017), wet–dry cycling (Doran et al., 2019; Forsythe et al., 2015; Frenkel-Pinter et al., 2019, 2022; Mamajanov et al., 2014), dynamic kinetic stability (Pascal and Pross, 2015; Pross and Pascal, 2013), and models of self-organization (Chvykov et al., 2021).

An instructive example of chemical evolution is provided by the molecular transformations mediated by ester–amide exchange, in which relatively labile ester linkages are replaced by kinetically trapped amide bonds (Fig. 5). In one example that involves the co-oligomerization of amino acids and hydroxy acids to form depsipeptides (oligomers with both ester and amide backbone linkages), the oligomeric products change over time from more ester-rich backbones to more amide-rich backbones (Forsythe et al., 2015). A similar process occurs with mixtures of amino acids and mercaptoacids, which oligomerize during wet–dry cycling to form thiodepsipeptides that contain mixed thioester and amide bonds (Fig. 5) (Frenkel-Pinter et al., 2022). In addition to depsipeptides and thiodepsipeptides, ester–amide exchange can also occur between amino acids and ester bond-containing lipids under wet–dry cycling conditions to form amphiphilic molecules called N-acyl amino acids, which have the ability to self-assemble into membrane compartments (Joshi et al., 2021a, 2022).

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FIG. 5.

Polymer evolution via ester-amide exchange. (a) Chemical structures of polypeptide, polyester, depsipeptide, and thiodepsipeptide backbones. (b) Chemical evolution in mixtures containing hydroxy acids and amino acids. Esters, formed by condensation–dehydration reactions between hydroxy acids, are converted to depsipeptides by ester–amide exchange with an amino acid. (c) Chemical evolution in mixtures containing mercaptoacids, hydroxy acids, and amino acids. Thioesters, formed by condensation–dehydration reactions between mercaptoacids, are converted to esters by thioester–ester exchange with a hydroxy acid, which are then converted to amides via ester–amide exchange with an amino acid. This image was adapted from Frenkel-Pinter et al. (2019), CC BY-NC-ND 4.0.

A number of potentially prebiotic processes have been demonstrated to drive chemical evolution. The process best studied is wet–dry cycling as a model of geochemical/geophysical energy flux (Damer and Deamer, 2020; Forsythe et al., 2015; Lahav et al., 1978; Mamajanov, 2019; New and Pohorille, 2000; Ross and Deamer, 2016). Water activity on land cycles with the rotation of Earth (e.g., day–night cycles, seasonal fluctuations, activity at tidal pools), and wet–dry cycling causes oscillations between condensation of building-blocks to form oligomers in the dry phase and hydrolysis of oligomers into smaller fragments during the wet phase (Fig. 6). Wet–dry cycling provides a possible link between biochemistry (hydrolysis/condensation) and the environment (wet–dry). Reversible polymerization reactions in wet–dry cycling conditions are continuous nonequilibrium dynamic systems where chemical energy continuously flows; energy is absorbed through the formation of bonds during the dry phase and is dissipated through the hydrolysis of bonds during the wet phase.

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FIG. 6.

Schematic diagram showing a hypothetical process for synthesis and chemical selection of a structured (folded) polymer during wet–dry cycling. The relative temperature levels indicated are intended to illustrate that environmental variations at different points in the cycle could facilitate each of the steps required for polymer evolution to be driven by a geophysical wet–dry cycle. Other environmental variations that could facilitate such a cycle, in addition to temperature and water activity, include pH, ionic strength, and photon flux.

The process of chemical evolution en route to life would have been guided by chemical selection—the buildup or utilization of certain molecules based on environmentally suited chemical properties. We can imagine chemical selection having operated at every stage of the origin of life, and in a multifaceted way at each stage, including acting through (i) chemical inventory, (ii) chemical reactivity, (iii) combinatorial compression, (iv) molecular assembly, and (v) water chemistry (Fig. 7).

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FIG. 7.

Several mechanisms of chemical selection. The processes shown could lead to the buildup or preferential utilization of certain molecules based on environmentally suited chemical properties.

i.

Chemical inventory. The availability of a given molecule is the most fundamental requirement for its participation in chemical reaction networks. Thus, the prebiotic inventory of various building blocks, oligomers, and molecular assemblies is an essential (but poorly defined) aspect of prebiotic chemical selection. Studies into the availability and functioning of abiotic molecular systems are often (and understandably) inclined to focus on molecules involved in extant biology. However, it is likely that various heterogenous polymers and chimeras not found in extant life existed in early Earth’s chemical milieu before coded biopolymer synthesis. While different from today’s biopolymers, these proto-polymers might have played critical roles during chemical evolution and chemical selection leading to the selected polymers of life. Diverse functional proto-nucleic acids might have existed (Bhowmik and Krishnamurthy, 2019; Eschenmoser, 2011; Fialho et al., 2020, 2021; Trevino et al., 2011; Ura et al., 2009; Yadav et al., 2020). For example, the formation of depsipeptide nucleic acid analogs that can exhibit complementary self-assembly in aqueous solutions has been demonstrated (Fialho et al., 2021). Chimeras of mixed threose nucleic acid–RNA and RNA–DNA oligonucleotides act as templates to mediate the ligation of homogeneous backbone oligomers (Bhowmik and Krishnamurthy, 2019). In the context of proto-peptides, depsipeptides and thiodepsipeptides have been studied (Forsythe et al., 2015; Frenkel-Pinter et al., 2022).

Considering that complex mixtures of molecules existed on prebiotic Earth, it is likely that molecular cooperation existed from the very beginning in the form of both covalent and noncovalent interactions (Runnels et al., 2018). The ability of molecules to interact with other molecules in the same environment could have favored the selection, persistence, and emergence of certain cooperative subsets of molecules within the prebiotic milieu. For example, the close synergy between peptides and nucleic acids in biology is suggestive of a functional coevolution that could have begun with rudimentary, mutually stabilizing interactions at early stages of chemical evolution (Frenkel-Pinter et al., 2020a, 2020b; Kamat et al., 2015; Lahav, 1993; Pascal et al., 2005). Mutual stabilization has also been reported between fatty acids and other classes of molecules. For example, it was found that various nucleobases and sugars stabilize decanoic acid vesicles against salt-induced flocculation through noncovalent interactions (Black et al., 2013). Amino acids can also bind to and stabilize fatty acid membranes (Cornell et al., 2019). Moreover, a recent study revealed that interactions between decanoic acid and an amyloidogenic peptide (Orn-Val)₄ increase the stability of assembled structures (Bomba et al., 2018; Kwiatkowski et al., 2021). The dependence of biochemistry on metal ions appears to be ancient (Belmonte and Mansy, 2016; Frenkel-Pinter et al., 2020b). Metals are widely used as catalysts in biology; about one-third of all enzymes are metalloenzymes (Bartnikas and Gitlin, 2001). Metal ion-catalyzed peptide and RNA formation has been demonstrated (Frenkel-Pinter et al., 2021b; Kaddour et al., 2018; Leman et al., 2004; Lohrmann et al., 1980; Rode, 1999). Recent work showed that Mg²⁺ and several other metals increase the thermal stability of cysteine-containing peptides (Rossetto et al., 2022). Likewise, assembly of RNA with Mg²⁺ can promote RNA folding and stabilize RNA against hydrolysis (Guth-Metzler et al., 2023).

17. What Does the Future Hold for Understanding the Prebiotic Past?

Numerous exciting avenues are being pursued to understand the chemical origins of life. We feel that two areas in the study of prebiotic chemistry are especially likely to provide important advances for characterizing potential routes from small molecules to the emergence of functional polymers.

i.

Embracing systems chemistry. Systems chemistry is the study of networks of interacting molecules that give rise to emergent properties such as structure and function (Cafferty et al., 2019; Kriebisch et al., 2023; Krishnamurthy, 2020; Patel et al., 2015; Ritson and Sutherland, 2012; Ruiz-Mirazo et al., 2014). Since the prebiotic milieu was rich in molecules that could potentially interact, it is crucial to investigate the origin of life from a systems chemistry point of view. For example, in DCC, monomers can dynamically link, shuffle, and exchange between oligomers (Beierle et al., 2018; Lam et al., 2005; Li et al., 2013; Otto et al., 2002). DCC has achieved host–guest functionality (Lam et al., 2005; Otto et al., 2002), elaborate folds (Liu et al., 2019), and self-replication (Carnall et al., 2010). Studies of mutually catalytic systems (Vincent et al., 2019) and reproducing catalytic micelles (Kahana and Lancet, 2021) have revealed mechanistic information on chemical evolution. Functional molecules can be selected via autocatalytic production of macrocycles (Miao et al., 2021; Wołos et al., 2020). Wet–dry cycling led to efficient emergence of catalytic activity (specifically, esterase activity) in basic depsipeptide mixtures (Doran et al., 2019). As another function-related example, glycerol citrate polymer-supported ZnS nanocrystals have been shown to possess a high photocatalytic activity (Mamajanov et al., 2020).

ii.

More broadly studying alternative and heterogeneous polymers and assemblies containing them. It is not possible to overstate the importance of considering the possibility that life started with polymers other than those found in extant life. Biochemists began considering this possibility at least as early as 1971 when Alex Rich proposed that polyesters may have preceded polypeptides (Rich, 1971); his proposal was inspired by the greater ease by which polyesters can be made abiotically compared with polypeptides and the fact that the ribosome is also able to catalyze ester bond formation (Fahnestock and Rich, 1971). Similarly, after decades of searching for a possible abiotic synthesis for RNA, Leslie Orgel eventually embraced the possibility that RNA was preceded by a different informational polymer but conceded that this possibility was a “gloomy prospect,” because the possibility that life began with polymers no longer present in extant life opens up an enormous chemical space for the possible building blocks of the original polymers of life (Orgel, 1998). While an expanded chemical space is certainly a challenge, alternative building blocks also come with the potential to find chemistries that provide much more facile routes to polymers that could get life started and on an evolutionary path to today’s biopolymers. As discussed above, α-hydroxy acids are readily polymerized into polyesters, and mixing α-hydroxy acids with amino acids leads to depsipeptides (polymers containing both ester and amide backbone linkages). Likewise, exploration of various heterocycles as possible ancestors to the nucleobases of extant has revealed at least five heterocycles that readily form nucleosides with ribose (Fialho et al., 2020), a property not shared with the extant nucleobases, which do not form nucleosides with ribose, or in only minimal yields, even under the most favorable conditions. Furthermore, some of these possible proto-nucleobases have been demonstrated to form nucleoside-like glycosides with a variety of sugars (Fialho et al., 2018; Roche et al., 2023). Such experimental results, stemming from considering proto-biopolymers composed of alternatives to amino acids and RNA, illustrate how polymers similar but distinct from the current biopolymers could have arisen more readily on prebiotic Earth. Later, chemical and/or biological evolution would have led to the transition from easier-to-synthesize oligomers to those with greater functionality.

18. Conclusions

The transition from abiotic chemistry to life undoubtedly required numerous stages of chemical evolution, of which only a few are discussed here. Chemical selection would have occurred at every stage of the origin of life—including an initial selection of building blocks from those that were available and from those that could be oligomerized, followed by the down selection to oligomers that were able to persist, fold, assemble, and so on. It is likely that substantial enrichment of some molecular species over others was driven in part by an interplay of kinetics of oligomer synthesis and hydrolysis. As polymers almost certainly played a role in the transition from prebiotic chemistry to life, it is important to understand how prebiotic polymers could have emerged and interacted in mutually beneficial ways. There are numerous reported methods for coaxing building blocks abiotically into oligomers, which makes it likely that at least some of these processes could have occurred in different environments on early Earth. Molecular assembly of oligomers into noncovalent complexes would have provided further mechanisms for chemical persistence, selection, and emergence of new functions. A major unresolved challenge is to more fully explore chemical reactions and interactions within heterogeneous mixtures, processes of chemical evolution that may occur in these mixtures, and how possible predecessors to the building blocks of extant biopolymers may have assembled more easily into polymers that facilitated the emergence of functions, such as selective catalysis, that were necessary for the emergence of RNA, DNA, and the coded synthesis of proteins.

Authors’ Contributions

All authors contributed to the conceptualization, writing, and editing of the article.